In this study, a population of chromosome segment substitution lines （CSSLs） derived from the cross between 9311 （indica） and Nipponbare （japonica） was employed to map the quantitative trait loci （QTLs） for sa...In this study, a population of chromosome segment substitution lines （CSSLs） derived from the cross between 9311 （indica） and Nipponbare （japonica） was employed to map the quantitative trait loci （QTLs） for salt tolerance under the salt stress simulated with 0.5% NaCI, using survival rate as the index. The data were analyzed by QTL IciMapping v3.1, and the results showed that one QTL （QSsr3） related to salt tolerance was located in the vicinity of the marker RM1350 on chromosome 3, into a genetic interval of 113.2-132.8 cM, with a contribution rate of 17.75%. The additive effect was 10.9, indicating that the QTL derived from the parent Nipponbare improved the salt tolerance of rice at seedling stage. This study will provide a theoretical basis for the selection of salt tolerant rice germplasm.展开更多
Dissecting the genetic relationships among gluten-related traits is important for high quality wheat breeding. Quantita- tive trait loci （QTLs） analysis for gluten strength, as measured by sedimentation volume （SV...Dissecting the genetic relationships among gluten-related traits is important for high quality wheat breeding. Quantita- tive trait loci （QTLs） analysis for gluten strength, as measured by sedimentation volume （SV） and gluten index （GI）, was performed using the QTLNetwork 2.0 software. Recombinant inbred lines （RILs） derived from the winter wheat varieties Shannong 01-35xGaocheng 9411 were used for the study. A total of seven additive QTLs for gluten strength were identi- fied using an unconditional analysis. QGi1D-13 and QSv1D-14 were detected through unconditional and conditional QTLs mapping, which explained 9.15-45.08% of the phenotypic variation. QTLs only identified under conditional QTL mapping were located in three marker intervals： WPT-3743-GLU-D1 （1D）, WPT-7001-WMC258 （1B）, and WPT-8682-WPT-5562 （1B）. Six pairs of epistatic QTLs distributed nine chromosomes were identified. Of these, two main effect QTLs （QGi1D-13 and QSvlD-14） and 12 pairs of epistatic QTLs were involved in interactions with the environment. The results indicated that chromosomes 1B and 1D are important for the improvement of gluten strength in common wheat. The combination of conditional and unconditional QTLs mapping could be useful for a better understanding of the interdependence of different traits at the QTL molecular level.展开更多
In this study, a population of 119 chromosome segment substitution lines （CSSLs） derived from backcross between indica 9311 and japonica Nipponbare was employed to map quantitative trait loci （QTL） associated with...In this study, a population of 119 chromosome segment substitution lines （CSSLs） derived from backcross between indica 9311 and japonica Nipponbare was employed to map quantitative trait loci （QTL） associated with sheath blight resis-tance in rice with toothpick inoculation method. A total of three sheath blight resis-tance-associated QTLs （qsb8-1, qsb8-2 and qsb8-3） were identified, which were lo-cated on adjacent molecular markers RM3262, RM5485 and RM3496 of chromo-some 8; the genetic interval was 81.7cM-91.7cM, 91.7cM-108.1cM and 108.1cM-119.6cM, respectively. The additive effect of qsb8-2 was negative, indicating that sheath blight resistance of susceptible parent harboring qsb8-2 fragment was en-hanced; additive effects of qsb8-1 and qsb8-3 were positive, indicating that sheath blight resistance of susceptible parent harboring qsb8-1 and qsb8-3 fragments was reduced.展开更多
Current rice production is usually guaranteed by applying large amount of chemical nitrogen fertilizers to paddy soils. The improvement of nitrogen use efficiency is of great importance not only in rice production its...Current rice production is usually guaranteed by applying large amount of chemical nitrogen fertilizers to paddy soils. The improvement of nitrogen use efficiency is of great importance not only in rice production itself but in environmental protection as well. In this study we performed a molecular marker-based genetic analysis of nitrogen use efficiency for biomass production （NUEp） and several other related traits in a recombinant inbred line （RIL） population, derived from a cross of the parents of Shanyou 63, the most widely cultivated indica hybrid in China. A total of 12 QTLs were detected using interval mapping with a LOD threshold of 2.0, among which one QTL controlling NUEp was located at the marker interval of Waxy-C1496 on chromosome 6, and the rest 11 QTLs associated nitrogen concentration and accumulation in rice plant were positioned on chromosomes 1, 2, 4 and 6, respectively. Correlation between NUEp and other traits was analyzed and the implications of the results with respect to the improvement of the hybrid rice were discussed.展开更多
Huanglongbing(HLB)is the most devastating disease for citrus worldwide.Candidatus Liberibacter asiaticus(C Las),vectored by Asian citrus psyllid(ACP,Diaphorina citri Kuwayama),is the most common pathogen causing the d...Huanglongbing(HLB)is the most devastating disease for citrus worldwide.Candidatus Liberibacter asiaticus(C Las),vectored by Asian citrus psyllid(ACP,Diaphorina citri Kuwayama),is the most common pathogen causing the disease.Commercial citrus varieties are highly susceptible to HLB,whereas trifoliate orange(Poncirus trifoliata)is considered highly tolerant to HLB.An F1 segregating population and their parent trifoliate orange and sweet orange,which had been exposed to intense HLB pressure for three years,was evaluated for disease symptoms,ACP colonization,C Las titer and tree vigor repeatedly for two to three years.Trifoliate orange and sweet orange showed significant differences for most of the phenotypic traits,and the F1 population exhibited a large variation.A high-density SNP-based genetic map with 1402 markers was constructed for trifoliate orange,which exhibited high synteny and high coverage of its reference genome.A total of 26 quantitative trait locus(QTLs)were identified in four linkage groups LG-t6,LG-t7,LG-t8 and LG-t9,of which four QTL clusters exhibit a clear co-localization of QTLs associated with different traits.Through genome-wide analysis of gene expression in response to C Las infection in‘Flying Dragon’and‘Larger-Flower DPI-50-7’trifoliate orange,85 differentially expressed genes were found located within the QTL clusters.Among them,seven genes were classified as defense or immunity protein which exhibited the highest transcriptional change after C Las infection.Our results indicate a quantitative genetic nature of HLB tolerance and identified candidate genes that should be valuable for searching for genetic solutions to HLB through breeding or genetic engineering.展开更多
The lower seed setting is one of the major hindrances which face grain yield in rice. One of the main reasons to cause low spikelet fertility （seed setting） is male sterility or pollen abortion. Notably, pollen abor...The lower seed setting is one of the major hindrances which face grain yield in rice. One of the main reasons to cause low spikelet fertility （seed setting） is male sterility or pollen abortion. Notably, pollen abortion has been frequently observed in advanced progenies of rice. In the present study, 149 BC2F6 individuals with significant segregation in spikelet fertility were generated from the cross between N040212 （indica） and Nipponbare （japonica） and used for primary gene mapping. Three QTLs, qSS-1, qSS-7 and qSS-9 at chromosomes 1, 7 and 9, respectively, were found to be associated with seed setting. The recombinant analysis and the physical mapping information from publicly available resources exhibited that the qSS-1, qSS-7 and qSS-9 loci were mapped to an interval of 188, 701 and 3741 kb, respectively. The seed setting responsible for QTL qSS-1 was further fine mapped to 93.5 kb by using BC2F7 population of 1 849 individuals. There are 16 possible putative genes in this 93.5 kb region. Pollen vitality tests and artificial pollination indicated that the male gamete has abnormal pollen while the female gamete was normal. These data showed that low seed setting rate relative to qSS-1 may be caused by abnormal pollen grains. These results will be useful for cloning, functional analysis of the target gene governing spikelet fertility （seed setting） and understanding the genetic bases of pollen sterility.展开更多
It had been demonstrated that the strong and highly significant quantitative trait locus（QTL） can affect protein percentage on Bos Taurus Autosome 3（BTA3） at the position 52 cM, near the microsatellite DIK4353, wi...It had been demonstrated that the strong and highly significant quantitative trait locus（QTL） can affect protein percentage on Bos Taurus Autosome 3（BTA3） at the position 52 cM, near the microsatellite DIK4353, with the 95% confidence interval spanning from 25 to 57 cM in Chinese Holstein population using QTL-express, MQREML, and GRIDQTL softwares. This study herein focused on such region of fine mapping QTLs for milk production and functional traits with 16 microsatellite markers with coverage of 33 cM between the markers BMS2904 and MB099 on BTA3 in a daughter-designed Chinese Holstein population. A total of 1 298 Holstein cows and 7 sires were genotyped for 16 microsatellites with ABI 3700 DNA sequencer. The variance components QTL linkage analysis（LA） and linkage-disequilibrium（LD） analysis（LA/LD） was performed to map QTLs for 7 traits, i.e., 305-d milk yield, fat yield, protein yield, fat percentage, protein percentage, somatic cell score and persistency of milk yield. Four strong and highly significant QTLs were detected for fat yield, fat percentage, protein percentage and somatic cell score at the position 40, 30, 27 and 26 cM, respectively. Two minor QTLs for milk yield and persistency of milk yield were identified at 42 and 46 cM, respectively. These findings provided a general idea for the fine mapping of the causal mutation for milk production and functional traits on BTA3 in the future.展开更多
Cotton breeding for the development of early-maturing varieties is an effective way to improve multiple cropping indexes and alleviate the conflict between grains and cotton in the cultivated fields in China.In the pr...Cotton breeding for the development of early-maturing varieties is an effective way to improve multiple cropping indexes and alleviate the conflict between grains and cotton in the cultivated fields in China.In the present study,we aimed to identify upland cotton quantitative trait loci(QTLs)and candidate genes related to early-maturity traits,including whole growth period(WGP),flowering timing(FT),node of the first fruiting branch(NFFB),height of the node of the first fruiting branch(HNFFB),and plant height(PH).An early-maturing variety,CCRI50,and a latematuring variety,Guoxinmian 11,were crossed to obtain biparental populations.These populations were used to map QTLs for the early-maturity traits for two years(2020 and 2021).With BSA-seq analysis based on the data of population 2020,the candidate regions related to early maturity were found to be located on chromosome D03.We then developed 22 polymorphic insertions or deletions(InDel)markers to further narrow down the candidate regions,resulting in the detection of five and four QTLs in the 2020 and 2021 populations,respectively.According to the results of QTL mapping,two candidate regions(InDel_G286-InDel_G144 and InDel_G24-InDel_G43)were detected.In these regions,three genes(GH_D03G0451,GH_D03G0649,and GH_D03G1180)have nonsynonymous mutations in their exons and one gene(GH_D03G0450)has SNP variations in the upstream sequence between CCRI50 and Guoxinmian 11.These four genes also showed dominant expression in the floral organs.The expression levels of GH_D03G0451,GH_D03G0649 and GH_D03G1180 were significantly higher in CCRI50 than in Guoxinmian 11 during the bud differentiation stages,while GH_D03G0450 showed the opposite trend.Further functional verification of GH_D03G0451 indicated that the GH_D03G0451-silenced plants showed a delay in the flowering time.The results suggest that these are the candidate genes for cotton early maturity,and they may be used for breeding early-maturity cotton varieties.展开更多
In coffee breeding practice, two quantitative traits, namely cherry and green bean characters are the important phenotypic selection index. The synchronous of cherry maturation, size, weight and shape of green bean ar...In coffee breeding practice, two quantitative traits, namely cherry and green bean characters are the important phenotypic selection index. The synchronous of cherry maturation, size, weight and shape of green bean are desirable traits for the future breeding. In order to increase the breeding efficiency, a set of quantitative trait loci （QTLs） analysis controlling these traits was carried out. The QTL analysis was performanced in cross pollinated population of Coffea canephora using single nucleotide polymorphisms （SNPs） and simple sequence repeats （SSRs） markers. Totally 12 QTLs determined desirable cherry and green bean traits were identified on 9 linkage groups （LG）, where these QTLs mapped forming clusters in 11 different chromosomal regions. The desirable traits which can be detected by their QTLs are synchronous of cherry maturation （LG B and LG G）, cherry size （LG A, LG F and LG G）, bean shape （LG B, LG D and LG J）, bean weight （LG H）, bean size （LG A and LG E） and cherry-bean size （LG K） The gene action of these QTLs was dominance or an interaction of alleles （epistasis between alleles at the studied locus） effect. The yielded linkage map and the detected QTL can provide a tool for further genetic analysis of two traits and be potential for maker-assisted selection in C. canephora breeding.展开更多
Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq ...Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F_(3)populations offering notable advantages over F2populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading(DTH) in a 7200-plant rice F_(3)population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F_(3)populations and multi-environment experiments can achieve high power, resolution, and reliability.展开更多
The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and starch.Nevertheless,the genetic basis underlying these nutritional quality traits...The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and starch.Nevertheless,the genetic basis underlying these nutritional quality traits during grainfilling remains poorly understood.In this study,the concentrations of protein,oil,and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages post-pollination.All the traits exhibited considerable phenotypic variation.During the grain-filling stage,the levels of protein and starch content generally increased,whereas oil content decreased,with significant changes observed between 30 and 40 days after pollination.Quantitative trait locus(QTL)mapping was conducted and a total of 32 QTLs,comprising 14,12,and 6 QTLs for grain protein,oil,and starch content were detected,respectively.Few QTLs were consistently detectable across different time points.By integrating QTL analysis,glo-bal gene expression profiling,and comparative genomics,we identified 157,86,and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein,oil,and starch con-tent,respectively.Subsequent gene function annotation prioritized 15 candidate genes potentially involved in reg-ulating grain quality traits,including those encoding transcription factors(NAC,MADS-box,bZIP,and MYB),cell wall invertase,cellulose-synthase-like protein,cell division cycle protein,trehalase,auxin-responsive factor,and phloem protein 2-A13.Our study offers significant insights into the genetic architecture of maize kernel nutritional quality and identifies promising QTLs and candidate genes,which are crucial for the genetic enhance-ment of these traits in maize breeding programs.展开更多
A population of 180 recombinant inbred lines （RILs） was developed by single seed descended from the cross of high yield Upland cotton （Gossypium hirsutum L.） varieties Zhongmiansuo12 （ZMSI2） and 8891, the two pa...A population of 180 recombinant inbred lines （RILs） was developed by single seed descended from the cross of high yield Upland cotton （Gossypium hirsutum L.） varieties Zhongmiansuo12 （ZMSI2） and 8891, the two parents of Xiangzamian2 （XZM2）. A genetic linkage map consisting of 132 loci and covering 865.20 cM was constructed using the RIL population chiefly with SSR markers. Yield and yield components were investigated for RILs in three environments in China. The purpose of the present research was to analyze the relationship between yield and its components and to map QTL for yield and yield components in cotton. QTL were tagged with data sets from single environment （separate analysis） and a set of data from means of the three environments （joint analysis）. A total of 34 QTL for yield and yield components were independently detected in three environments, whereas fifteen QTL were found in joint analysis. Notably, a stable lint percentage QTL qLP-A10-1 was detected both in joint analysis and in two environments of separate analysis, which might be of special value for marker-assisted selection. The QTL detected in the present study provide new information on improving yield and yield components. Results of path analysis showed that bolls/plant had the largest contribution to lint yield, which is consistent with the mid-parent heterosis value in F1. Accordingly, in cotton breeding, bolls/plant can be considered first and other yield components measured as a whole to implement variety enhancement and hybrid selection of cotton.展开更多
Gossypium hirsutum L. and G. barbadense L. are the two cultivated tetraploid species of cotton. The first is characterized by a high yield and wide adaptation, and the second by its super fiber property. Substit...Gossypium hirsutum L. and G. barbadense L. are the two cultivated tetraploid species of cotton. The first is characterized by a high yield and wide adaptation, and the second by its super fiber property. Substitution line in which a pair of intact chromosomes of TM_1 ( G. hirsutum ) were replaced by a pair of homozygous chromosomes of 3_79 ( G. barbadense ) is an excellent material for genetic research and molecular tagging. In this study, substitution line 16 (Sub 16) was used to evaluate the performance of the 16th chromosome in G. barbadense in TM_1 background. The genetic analysis using the major gene plus polygene mixed inheritance model in F 2∶3 family revealed that there might exist 2 QTLs respectively for boll size, lint percentage, lint index, fiber length and the first fruit branch node, 1 QTL for fiber elongation and flowering date, and no QTL for seed index, fiber strength and Micronaire in chromosome 16. However, 9 QTLs (LOD (logarithm of odds)≥3.0) controlling 6 quantitative traits were significantly identified in linkage group of chromosome 16 constructed in (TM_1×3_79) F 2by interval mapping. Among them, 1 QTL for boll size, fiber length, flowering date and fiber elongation could explain 15.2%, 19.7%, 12.1%, and 11.7% phenotypic variance respectively, 2 QTLs for lint index could explain 11.6% and 41.9%, and 3 QTLs for lint percentage could explain 8.7%, 9.6% and 29.2% phenotypic variance respectively. One unlinked SSR marker was associated with one QTL respectively for boll size and flowering date and they could explain 1.60% and 4.63% phenotypic variance. The traits associated significantly with chromosome 16 from Sub 16 were boll weight, lint percentage, lint index, fiber length, fiber elongation and flowering days.展开更多
Grain cooking and nutrient qualities are the most important components of rice （Oryza sativa L.） quality. A doubled haploid （DH） population from a cross between two japonica cultivars was used to examine the pheno...Grain cooking and nutrient qualities are the most important components of rice （Oryza sativa L.） quality. A doubled haploid （DH） population from a cross between two japonica cultivars was used to examine the phenotypic values and potential QTLs for the quality traits. The cooking and nutrient quality traits, including the amylose content （AC）, the gel consistency （CJC）, the gelatinization temperature （GT）, and the protein content （PC）, in rice grown under upland and lowland environments were evaluated. Significant differences for AC, GC, GT, and PC between upland and lowland environments were detected. The phenotypic values of all four traits were higher under upland environment than lowland environment. The value of PC under upland environment was significantly higher （by 37.9%） than that under lowland environment. This suggests that upland cultivation had large effect on both cooking and nutrient qualifies. A total of seven QTLs and twelve pairs of QTLs were detected to have significant additive and epistatic effects for the four traits. Significant Q x E interaction effects of two QTLs and two pairs of QTLs were also discovered. The general contribution of additive QTLs ranged from 1.91% to 19.77%. The Q × E interactions of QTLs QGt3 and QAc6 accounted for 8.99% and 47.86% of the phenotypic variation, respectively, whereas those of the 2 pairs of epistatic QTLs, QAc6-QAcllb and QAc8-QAc9, accounted for 32.54% and 11.82%, respectively. Five QTLs QGt6b, QGt8, QGt11, QGcl, and QPc2, which had relatively high general contribution and no Q x E interactions, were selected to facilitate the upland rice grain quality breeding.展开更多
A statistical method for mapping quantitative trait loci （QTLs） underlying endosperm traits is proposed. The method is based on a genetic model containing both the direct effects and maternal effects of an endosperm...A statistical method for mapping quantitative trait loci （QTLs） underlying endosperm traits is proposed. The method is based on a genetic model containing both the direct effects and maternal effects of an endosperm QTL and on an experimental design termed two-stage hierarchical design, in which the trait information is obtained from F3 endosperms and molecular marker information is obtained from F2 plants and F3 embryos （plants）. Results of computer simulations indicate that the method can efficiently map endosperm QTLs and precisely estimate both the direct and maternal effects of endosperm QTLs when the sample size is sufficiently large.展开更多
The variation of seedling characteristics under different water supply conditions is strongly associated with drought resistance in rice （Oryza sativa L.） and a better elucidation of its genetics is helpful for impr...The variation of seedling characteristics under different water supply conditions is strongly associated with drought resistance in rice （Oryza sativa L.） and a better elucidation of its genetics is helpful for improving rice drought resistance. Ninety-six doubled-haploid （DH） rice lines of an indica and japonica cross were grown in both flooding and upland conditions and QTLs for morphological traits at seedling stage were examined using 208 restriction fragment length polymorphism （RFLP） and 76 microsatellite （SSR） markers. A total of 32 putative QTLs were associated with the four seedling traits： average of three adventitious root lengths （ARL）, shoot height （SH）, shoot biomass （SW）, and root to shoot dry weight ratio （RSR）. Five QTLs detected were the same under control and upland conditions. The ratio between the mean value of the seedling trait under upland and flooding conditions was used for assessing drought tolerance. A total of six QTLs for drought tolerance were detected. Comparative analysis was performed for the QTLs detected in this case and those reported from two other populations with the same upland rice variety Azucena as parent. Several identical QTLs for seedling elongation across the three populations with the positive alleles from the upland rice Azucena were detected, which suggests that the alleles of Azucena might be involved in water stress-accelerated elongation of rice under different genetic backgrounds. Five cell wall-related candidate genes for OsEXPI, OsEXP2, OsEXP4, EXT, and EGase were mapped on the intervals carrying the QTLs for seedling traits.展开更多
Segregation analysis of the mixed genetic model of major gene plus polygene was used to identify the major genes for cotton yield-related traits using six generations P1, P2, F1, B1, B2, and F2 generated from the cros...Segregation analysis of the mixed genetic model of major gene plus polygene was used to identify the major genes for cotton yield-related traits using six generations P1, P2, F1, B1, B2, and F2 generated from the cross of Baimian 1 x TM-1. In addition to boll size and seed index, the major genes for the other five traits were detected： one each for seed yield, lint percentage, boll number, lint index; and two for lint yield. Quantitative trait locus/loci （QTL） mapping was performed in the F2 and F2：3 populations of above cross through molecular marker technology, and a total of 50 QTL （26 suggestive and 24 significant） for yield-related traits were detected. Four common QTL were discovered： qLP-3b（F2）/qLP-3（F2：3） and qLP-19b （F2）/qLP-19（F2：3） for lint percentage, qBN-17（F2）/qBN-17（F2：3） for boll number, and qBS-26b（F2）/qBS-26（F2：3） for boll size. Especially, qLP- 3b（Fz）/qLP-3（F2：3）, not only had LOD scores 〉3 but also exceeded the permutation threshold （5.13 and 5.29, respectively）, correspondingly explaining 23.47 and 29.55% of phenotypic variation. This QTL should be considered preferentially in marker assisted selection （MAS）. Segregation analysis and QTL mapping could mutually complement and verify, which provides a theoretical basis for genetic improvement of cotton yield-related traits by using major genes （QTL）.展开更多
To gain insight into the molecular and genetic basis of fruit size and shape in cucumber,we conducted Quantitative Trait Locus(QTL)mapping with F2 and BC1F1 populations derived froma cross between the Northern-China t...To gain insight into the molecular and genetic basis of fruit size and shape in cucumber,we conducted Quantitative Trait Locus(QTL)mapping with F2 and BC1F1 populations derived froma cross between the Northern-China type inbred line CNS21 and the Southern-China type inbred line RNS7.Populations were evaluated during two developmental stages,ovary at anthesis and commercial fruit(immature fruit).A total of 13 major-effect QTLs(R2>10%)were detected for six traits,and one of them,fruit shape index 2.1,explained more than 50%of phenotypic variation.All QTLs distributed on chromosome(chr)1 and 2.We constructed a physical map containing almost all of the QTLs with their physical location from previous studies.For fruit size and shape,the highest number of QTLs were mapped on chr1 and chr6,and the fewest number were mapped on chr2 and chr7.At least one consensus region was presented on each chromosome.In addition,three candidate genes were predicted between the long-fruited and round-fruited inbred lines by comparing the sequences of the consensus region of chr3,where many QTLs for marketable fruit length had been detected.Our results provide a base for additional QTLs and molecular markers for fruit size and shape in cucumber breeding.展开更多
Asiatic cotton （Gossypium arboreum L.） is an Old World cultivated cotton species. The sinense race was planted extensively in China. Due to the advances in spinning technology during the last century, the species wa...Asiatic cotton （Gossypium arboreum L.） is an Old World cultivated cotton species. The sinense race was planted extensively in China. Due to the advances in spinning technology during the last century, the species was replaced by the New World allotetraploid cotton G. hirsutum L. Gossypium arboreum is still grown in India and Pakistan and also used as an elite in current cotton breeding programs. In addition, G. arboreum serves as a model for genomic research in Gossypium. In the present study, we generated an A-genome diploid cotton intraspecific genetic map including 264 SSR loci with three morphological markers mapped to 13 linkage groups. The map spans 2,508.71 cM with an average distance of 9.4 cM between adjacent loci. A population containing 176 F2：3 families was used to perform quantitative trait loci （QTL） mapping for 17 phenotypes using Multiple QTL Model （MQM） of MapQTL ver 5.0. Overall, 108 QTLs were detected on 13 chromosomes. Thirty-one QTLs for yield and its components were detected in the F2 population. Forty-one QTLs for yield and its components were detected in the F2：3 families with a total of 43 QTLs for fiber qualities. Two QTLs for seed cotton weight/plant and lint index and three QTLs for seed index were consistently detected both in F2 and F2：3. Most QTLs for fiber qualities and yields were located at the same interval or neighboring intervals. These results indicated that the negative correlation between fiber qualities and yield traits may result from either pleiotropic effect of one gene or linkage effects of multiple closely linked genes.展开更多
Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 0242...Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 02428 and YZX,two cultivars differing in vigor during early seedling growth,was used for QTL analysis.Nine traits associated with ESV were examined using a high-density map.Of 16 additive loci identified,three were detected in two generations and thus considered stable.Four epistatic interactions were detected,one of which was repeated in two generations.Further analysis of the pyramiding effect of the three stable QTL showed that the phenotypic value could be effectively improved with an increasing number of QTL.These results were combined with results from our previous QTL analysis of the germination index.The lines G58 and G182 combined all the favourable alleles of all three stable QTL for ESV and three QTL for germination speed.These two lines showed rapid germination and strong ESV.A total of 37 candidate differentially expressed genes were obtained from the regions of the three stable QTL by analysis of the dynamic transcriptomic expression profile during the seedling growth period of the two parents.The QTL are targets for ESV breeding and the candidate genes await functional validation.This study provides a theoretical basis and a genetic resource for the breeding of directseeded rice.展开更多
文摘In this study, a population of chromosome segment substitution lines （CSSLs） derived from the cross between 9311 （indica） and Nipponbare （japonica） was employed to map the quantitative trait loci （QTLs） for salt tolerance under the salt stress simulated with 0.5% NaCI, using survival rate as the index. The data were analyzed by QTL IciMapping v3.1, and the results showed that one QTL （QSsr3） related to salt tolerance was located in the vicinity of the marker RM1350 on chromosome 3, into a genetic interval of 113.2-132.8 cM, with a contribution rate of 17.75%. The additive effect was 10.9, indicating that the QTL derived from the parent Nipponbare improved the salt tolerance of rice at seedling stage. This study will provide a theoretical basis for the selection of salt tolerant rice germplasm.
基金support from the Natural Science Foundation of Shandong Province,China (ZR2015CM036)the Molecular Foundation of Main Crop Quality,the Ministry of Science and Technology of China (2016YFD0100500)+1 种基金the Project of Science and Technology of Shandong “Wheat Breeding by Molecular Design”,China (2016LZGC023)the Research Fund for Agricultural Big Data Project,China
文摘Dissecting the genetic relationships among gluten-related traits is important for high quality wheat breeding. Quantita- tive trait loci （QTLs） analysis for gluten strength, as measured by sedimentation volume （SV） and gluten index （GI）, was performed using the QTLNetwork 2.0 software. Recombinant inbred lines （RILs） derived from the winter wheat varieties Shannong 01-35xGaocheng 9411 were used for the study. A total of seven additive QTLs for gluten strength were identi- fied using an unconditional analysis. QGi1D-13 and QSv1D-14 were detected through unconditional and conditional QTLs mapping, which explained 9.15-45.08% of the phenotypic variation. QTLs only identified under conditional QTL mapping were located in three marker intervals： WPT-3743-GLU-D1 （1D）, WPT-7001-WMC258 （1B）, and WPT-8682-WPT-5562 （1B）. Six pairs of epistatic QTLs distributed nine chromosomes were identified. Of these, two main effect QTLs （QGi1D-13 and QSvlD-14） and 12 pairs of epistatic QTLs were involved in interactions with the environment. The results indicated that chromosomes 1B and 1D are important for the improvement of gluten strength in common wheat. The combination of conditional and unconditional QTLs mapping could be useful for a better understanding of the interdependence of different traits at the QTL molecular level.
基金Supported by Specific Fund for the Independent Innovation of Agricultural Science and Technology[CX(11)1020]~~
文摘In this study, a population of 119 chromosome segment substitution lines （CSSLs） derived from backcross between indica 9311 and japonica Nipponbare was employed to map quantitative trait loci （QTL） associated with sheath blight resis-tance in rice with toothpick inoculation method. A total of three sheath blight resis-tance-associated QTLs （qsb8-1, qsb8-2 and qsb8-3） were identified, which were lo-cated on adjacent molecular markers RM3262, RM5485 and RM3496 of chromo-some 8; the genetic interval was 81.7cM-91.7cM, 91.7cM-108.1cM and 108.1cM-119.6cM, respectively. The additive effect of qsb8-2 was negative, indicating that sheath blight resistance of susceptible parent harboring qsb8-2 fragment was en-hanced; additive effects of qsb8-1 and qsb8-3 were positive, indicating that sheath blight resistance of susceptible parent harboring qsb8-1 and qsb8-3 fragments was reduced.
基金This research was financially supported by the National Natural Science Foundation of China(NSFC)fund from the Education Committee of Jiangsu Province,China.The recombinant inbred line(RIL)population,derived from a cross of the parents of Shanyou 63,and relevant genetic information were provided by the National Key Lab for Crop Genetic Improvement of China.
文摘Current rice production is usually guaranteed by applying large amount of chemical nitrogen fertilizers to paddy soils. The improvement of nitrogen use efficiency is of great importance not only in rice production itself but in environmental protection as well. In this study we performed a molecular marker-based genetic analysis of nitrogen use efficiency for biomass production （NUEp） and several other related traits in a recombinant inbred line （RIL） population, derived from a cross of the parents of Shanyou 63, the most widely cultivated indica hybrid in China. A total of 12 QTLs were detected using interval mapping with a LOD threshold of 2.0, among which one QTL controlling NUEp was located at the marker interval of Waxy-C1496 on chromosome 6, and the rest 11 QTLs associated nitrogen concentration and accumulation in rice plant were positioned on chromosomes 1, 2, 4 and 6, respectively. Correlation between NUEp and other traits was analyzed and the implications of the results with respect to the improvement of the hybrid rice were discussed.
基金supported by grants from the Citrus Research and Development Foundation,USA(Grant No.CRDF#15-010)the New Varieties Development and Management Corporation(NVDMC),on behalf of the Florida citrus industry,USA,the Fundamental Research Funds for the Central Universities,China(Grant No.2022CDJXY-004)from the USDA-NIFA-SCRI,USA(Grant No.2015-70016-2302).
文摘Huanglongbing(HLB)is the most devastating disease for citrus worldwide.Candidatus Liberibacter asiaticus(C Las),vectored by Asian citrus psyllid(ACP,Diaphorina citri Kuwayama),is the most common pathogen causing the disease.Commercial citrus varieties are highly susceptible to HLB,whereas trifoliate orange(Poncirus trifoliata)is considered highly tolerant to HLB.An F1 segregating population and their parent trifoliate orange and sweet orange,which had been exposed to intense HLB pressure for three years,was evaluated for disease symptoms,ACP colonization,C Las titer and tree vigor repeatedly for two to three years.Trifoliate orange and sweet orange showed significant differences for most of the phenotypic traits,and the F1 population exhibited a large variation.A high-density SNP-based genetic map with 1402 markers was constructed for trifoliate orange,which exhibited high synteny and high coverage of its reference genome.A total of 26 quantitative trait locus(QTLs)were identified in four linkage groups LG-t6,LG-t7,LG-t8 and LG-t9,of which four QTL clusters exhibit a clear co-localization of QTLs associated with different traits.Through genome-wide analysis of gene expression in response to C Las infection in‘Flying Dragon’and‘Larger-Flower DPI-50-7’trifoliate orange,85 differentially expressed genes were found located within the QTL clusters.Among them,seven genes were classified as defense or immunity protein which exhibited the highest transcriptional change after C Las infection.Our results indicate a quantitative genetic nature of HLB tolerance and identified candidate genes that should be valuable for searching for genetic solutions to HLB through breeding or genetic engineering.
基金supported by the National Key Technologies R&D Program of China during the 12th Five-Year Plan period (2013BAD01B02-15 and 2015BAD02B01)the 948 Project of Minstry of Agriculture, China (2011-G2B and 2011-G1 (2)-25)
文摘The lower seed setting is one of the major hindrances which face grain yield in rice. One of the main reasons to cause low spikelet fertility （seed setting） is male sterility or pollen abortion. Notably, pollen abortion has been frequently observed in advanced progenies of rice. In the present study, 149 BC2F6 individuals with significant segregation in spikelet fertility were generated from the cross between N040212 （indica） and Nipponbare （japonica） and used for primary gene mapping. Three QTLs, qSS-1, qSS-7 and qSS-9 at chromosomes 1, 7 and 9, respectively, were found to be associated with seed setting. The recombinant analysis and the physical mapping information from publicly available resources exhibited that the qSS-1, qSS-7 and qSS-9 loci were mapped to an interval of 188, 701 and 3741 kb, respectively. The seed setting responsible for QTL qSS-1 was further fine mapped to 93.5 kb by using BC2F7 population of 1 849 individuals. There are 16 possible putative genes in this 93.5 kb region. Pollen vitality tests and artificial pollination indicated that the male gamete has abnormal pollen while the female gamete was normal. These data showed that low seed setting rate relative to qSS-1 may be caused by abnormal pollen grains. These results will be useful for cloning, functional analysis of the target gene governing spikelet fertility （seed setting） and understanding the genetic bases of pollen sterility.
基金supported by the High Technology Research and Development Program of China(2013AA102504)the Beijing Innovation Team of Technology System in the National Dairy Industry+2 种基金the National Key Technologies R&D Program of China(2011BAD28B02,2012BAD12B01)the Beijing Research and Technology Program,China(D121100003312001)the Program for Changjiang Scholar and Innovation Research Team in University,China(IRT1191)
文摘It had been demonstrated that the strong and highly significant quantitative trait locus（QTL） can affect protein percentage on Bos Taurus Autosome 3（BTA3） at the position 52 cM, near the microsatellite DIK4353, with the 95% confidence interval spanning from 25 to 57 cM in Chinese Holstein population using QTL-express, MQREML, and GRIDQTL softwares. This study herein focused on such region of fine mapping QTLs for milk production and functional traits with 16 microsatellite markers with coverage of 33 cM between the markers BMS2904 and MB099 on BTA3 in a daughter-designed Chinese Holstein population. A total of 1 298 Holstein cows and 7 sires were genotyped for 16 microsatellites with ABI 3700 DNA sequencer. The variance components QTL linkage analysis（LA） and linkage-disequilibrium（LD） analysis（LA/LD） was performed to map QTLs for 7 traits, i.e., 305-d milk yield, fat yield, protein yield, fat percentage, protein percentage, somatic cell score and persistency of milk yield. Four strong and highly significant QTLs were detected for fat yield, fat percentage, protein percentage and somatic cell score at the position 40, 30, 27 and 26 cM, respectively. Two minor QTLs for milk yield and persistency of milk yield were identified at 42 and 46 cM, respectively. These findings provided a general idea for the fine mapping of the causal mutation for milk production and functional traits on BTA3 in the future.
基金funded by the Natural Science Foundation of Xinjiang Uygur Autonomous Region,China(2022D01B222)the China Agriculture Research System(CARS-15-06)the Key R&D Project of Eight Division of Xinjiang Production and Construction Corps,China(2021NY01)。
文摘Cotton breeding for the development of early-maturing varieties is an effective way to improve multiple cropping indexes and alleviate the conflict between grains and cotton in the cultivated fields in China.In the present study,we aimed to identify upland cotton quantitative trait loci(QTLs)and candidate genes related to early-maturity traits,including whole growth period(WGP),flowering timing(FT),node of the first fruiting branch(NFFB),height of the node of the first fruiting branch(HNFFB),and plant height(PH).An early-maturing variety,CCRI50,and a latematuring variety,Guoxinmian 11,were crossed to obtain biparental populations.These populations were used to map QTLs for the early-maturity traits for two years(2020 and 2021).With BSA-seq analysis based on the data of population 2020,the candidate regions related to early maturity were found to be located on chromosome D03.We then developed 22 polymorphic insertions or deletions(InDel)markers to further narrow down the candidate regions,resulting in the detection of five and four QTLs in the 2020 and 2021 populations,respectively.According to the results of QTL mapping,two candidate regions(InDel_G286-InDel_G144 and InDel_G24-InDel_G43)were detected.In these regions,three genes(GH_D03G0451,GH_D03G0649,and GH_D03G1180)have nonsynonymous mutations in their exons and one gene(GH_D03G0450)has SNP variations in the upstream sequence between CCRI50 and Guoxinmian 11.These four genes also showed dominant expression in the floral organs.The expression levels of GH_D03G0451,GH_D03G0649 and GH_D03G1180 were significantly higher in CCRI50 than in Guoxinmian 11 during the bud differentiation stages,while GH_D03G0450 showed the opposite trend.Further functional verification of GH_D03G0451 indicated that the GH_D03G0451-silenced plants showed a delay in the flowering time.The results suggest that these are the candidate genes for cotton early maturity,and they may be used for breeding early-maturity cotton varieties.
文摘In coffee breeding practice, two quantitative traits, namely cherry and green bean characters are the important phenotypic selection index. The synchronous of cherry maturation, size, weight and shape of green bean are desirable traits for the future breeding. In order to increase the breeding efficiency, a set of quantitative trait loci （QTLs） analysis controlling these traits was carried out. The QTL analysis was performanced in cross pollinated population of Coffea canephora using single nucleotide polymorphisms （SNPs） and simple sequence repeats （SSRs） markers. Totally 12 QTLs determined desirable cherry and green bean traits were identified on 9 linkage groups （LG）, where these QTLs mapped forming clusters in 11 different chromosomal regions. The desirable traits which can be detected by their QTLs are synchronous of cherry maturation （LG B and LG G）, cherry size （LG A, LG F and LG G）, bean shape （LG B, LG D and LG J）, bean weight （LG H）, bean size （LG A and LG E） and cherry-bean size （LG K） The gene action of these QTLs was dominance or an interaction of alleles （epistasis between alleles at the studied locus） effect. The yielded linkage map and the detected QTL can provide a tool for further genetic analysis of two traits and be potential for maker-assisted selection in C. canephora breeding.
基金supported by Natural Science Foundation of Fujian Province (CN) (2020I0009, 2022J01596)Cooperation Project on University Industry-Education-Research of Fujian Provincial Science and Technology Plan (CN) (2022N5011)+1 种基金Lancang-Mekong Cooperation Special Fund (2017-2020)International Sci-Tech Cooperation and Communication Program of Fujian Agriculture and Forestry University (KXGH17014)。
文摘Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F_(3)populations offering notable advantages over F2populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading(DTH) in a 7200-plant rice F_(3)population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F_(3)populations and multi-environment experiments can achieve high power, resolution, and reliability.
基金supported by the Key Research and Development Program of Jiangsu Province(BE2022343)the Seed Industry Revitalization Project of Jiangsu Province(JBGS[2021]009)+2 种基金the National Natural Science Foundation of China(32061143030 and 31972487)Jiangsu Province University Basic Science Research Project(21KJA210002)the Innovative Research Team of Universities in Jiangsu Province,the High-End Talent Project of Yangzhou University,the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD),and Qing Lan Project of Jiangsu Province.
文摘The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and starch.Nevertheless,the genetic basis underlying these nutritional quality traits during grainfilling remains poorly understood.In this study,the concentrations of protein,oil,and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages post-pollination.All the traits exhibited considerable phenotypic variation.During the grain-filling stage,the levels of protein and starch content generally increased,whereas oil content decreased,with significant changes observed between 30 and 40 days after pollination.Quantitative trait locus(QTL)mapping was conducted and a total of 32 QTLs,comprising 14,12,and 6 QTLs for grain protein,oil,and starch content were detected,respectively.Few QTLs were consistently detectable across different time points.By integrating QTL analysis,glo-bal gene expression profiling,and comparative genomics,we identified 157,86,and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein,oil,and starch con-tent,respectively.Subsequent gene function annotation prioritized 15 candidate genes potentially involved in reg-ulating grain quality traits,including those encoding transcription factors(NAC,MADS-box,bZIP,and MYB),cell wall invertase,cellulose-synthase-like protein,cell division cycle protein,trehalase,auxin-responsive factor,and phloem protein 2-A13.Our study offers significant insights into the genetic architecture of maize kernel nutritional quality and identifies promising QTLs and candidate genes,which are crucial for the genetic enhance-ment of these traits in maize breeding programs.
基金This work was supported by the National Science Foundation for Outstanding Youth Scholars (No. 30025029), Chinese National Programs for High Technology Research and Development (No. 2002AA207006), the Teaching and Research Award Program for Outstanding Young Teachers in Higher Education Institutions, and Program for Changjiang Scholars and Innovative Research Team in University of MOE, China.
文摘A population of 180 recombinant inbred lines （RILs） was developed by single seed descended from the cross of high yield Upland cotton （Gossypium hirsutum L.） varieties Zhongmiansuo12 （ZMSI2） and 8891, the two parents of Xiangzamian2 （XZM2）. A genetic linkage map consisting of 132 loci and covering 865.20 cM was constructed using the RIL population chiefly with SSR markers. Yield and yield components were investigated for RILs in three environments in China. The purpose of the present research was to analyze the relationship between yield and its components and to map QTL for yield and yield components in cotton. QTL were tagged with data sets from single environment （separate analysis） and a set of data from means of the three environments （joint analysis）. A total of 34 QTL for yield and yield components were independently detected in three environments, whereas fifteen QTL were found in joint analysis. Notably, a stable lint percentage QTL qLP-A10-1 was detected both in joint analysis and in two environments of separate analysis, which might be of special value for marker-assisted selection. The QTL detected in the present study provide new information on improving yield and yield components. Results of path analysis showed that bolls/plant had the largest contribution to lint yield, which is consistent with the mid-parent heterosis value in F1. Accordingly, in cotton breeding, bolls/plant can be considered first and other yield components measured as a whole to implement variety enhancement and hybrid selection of cotton.
文摘Gossypium hirsutum L. and G. barbadense L. are the two cultivated tetraploid species of cotton. The first is characterized by a high yield and wide adaptation, and the second by its super fiber property. Substitution line in which a pair of intact chromosomes of TM_1 ( G. hirsutum ) were replaced by a pair of homozygous chromosomes of 3_79 ( G. barbadense ) is an excellent material for genetic research and molecular tagging. In this study, substitution line 16 (Sub 16) was used to evaluate the performance of the 16th chromosome in G. barbadense in TM_1 background. The genetic analysis using the major gene plus polygene mixed inheritance model in F 2∶3 family revealed that there might exist 2 QTLs respectively for boll size, lint percentage, lint index, fiber length and the first fruit branch node, 1 QTL for fiber elongation and flowering date, and no QTL for seed index, fiber strength and Micronaire in chromosome 16. However, 9 QTLs (LOD (logarithm of odds)≥3.0) controlling 6 quantitative traits were significantly identified in linkage group of chromosome 16 constructed in (TM_1×3_79) F 2by interval mapping. Among them, 1 QTL for boll size, fiber length, flowering date and fiber elongation could explain 15.2%, 19.7%, 12.1%, and 11.7% phenotypic variance respectively, 2 QTLs for lint index could explain 11.6% and 41.9%, and 3 QTLs for lint percentage could explain 8.7%, 9.6% and 29.2% phenotypic variance respectively. One unlinked SSR marker was associated with one QTL respectively for boll size and flowering date and they could explain 1.60% and 4.63% phenotypic variance. The traits associated significantly with chromosome 16 from Sub 16 were boll weight, lint percentage, lint index, fiber length, fiber elongation and flowering days.
基金This work was supported by the State Key Basic Research and Development Plan of China (973)the Hi-Tech Research and De-velopment Program of China (863) National Natural Science Foundation of China.
文摘Grain cooking and nutrient qualities are the most important components of rice （Oryza sativa L.） quality. A doubled haploid （DH） population from a cross between two japonica cultivars was used to examine the phenotypic values and potential QTLs for the quality traits. The cooking and nutrient quality traits, including the amylose content （AC）, the gel consistency （CJC）, the gelatinization temperature （GT）, and the protein content （PC）, in rice grown under upland and lowland environments were evaluated. Significant differences for AC, GC, GT, and PC between upland and lowland environments were detected. The phenotypic values of all four traits were higher under upland environment than lowland environment. The value of PC under upland environment was significantly higher （by 37.9%） than that under lowland environment. This suggests that upland cultivation had large effect on both cooking and nutrient qualifies. A total of seven QTLs and twelve pairs of QTLs were detected to have significant additive and epistatic effects for the four traits. Significant Q x E interaction effects of two QTLs and two pairs of QTLs were also discovered. The general contribution of additive QTLs ranged from 1.91% to 19.77%. The Q × E interactions of QTLs QGt3 and QAc6 accounted for 8.99% and 47.86% of the phenotypic variation, respectively, whereas those of the 2 pairs of epistatic QTLs, QAc6-QAcllb and QAc8-QAc9, accounted for 32.54% and 11.82%, respectively. Five QTLs QGt6b, QGt8, QGt11, QGcl, and QPc2, which had relatively high general contribution and no Q x E interactions, were selected to facilitate the upland rice grain quality breeding.
基金This work was supported by the Key Sci-Tech Project of Fujian Province (No. 2004NZ01-2) the Natural Science Foundation of Fujian Province of China (No. 2006J0300).
文摘A statistical method for mapping quantitative trait loci （QTLs） underlying endosperm traits is proposed. The method is based on a genetic model containing both the direct effects and maternal effects of an endosperm QTL and on an experimental design termed two-stage hierarchical design, in which the trait information is obtained from F3 endosperms and molecular marker information is obtained from F2 plants and F3 embryos （plants）. Results of computer simulations indicate that the method can efficiently map endosperm QTLs and precisely estimate both the direct and maternal effects of endosperm QTLs when the sample size is sufficiently large.
基金the National Key Basic Research Special Foundation of China (No. G1999011700) Zhejiang Provincial Natural Science Foundation of China (No. Y305314).
文摘The variation of seedling characteristics under different water supply conditions is strongly associated with drought resistance in rice （Oryza sativa L.） and a better elucidation of its genetics is helpful for improving rice drought resistance. Ninety-six doubled-haploid （DH） rice lines of an indica and japonica cross were grown in both flooding and upland conditions and QTLs for morphological traits at seedling stage were examined using 208 restriction fragment length polymorphism （RFLP） and 76 microsatellite （SSR） markers. A total of 32 putative QTLs were associated with the four seedling traits： average of three adventitious root lengths （ARL）, shoot height （SH）, shoot biomass （SW）, and root to shoot dry weight ratio （RSR）. Five QTLs detected were the same under control and upland conditions. The ratio between the mean value of the seedling trait under upland and flooding conditions was used for assessing drought tolerance. A total of six QTLs for drought tolerance were detected. Comparative analysis was performed for the QTLs detected in this case and those reported from two other populations with the same upland rice variety Azucena as parent. Several identical QTLs for seedling elongation across the three populations with the positive alleles from the upland rice Azucena were detected, which suggests that the alleles of Azucena might be involved in water stress-accelerated elongation of rice under different genetic backgrounds. Five cell wall-related candidate genes for OsEXPI, OsEXP2, OsEXP4, EXT, and EGase were mapped on the intervals carrying the QTLs for seedling traits.
基金supported by the National Natural Science Foundation of China(31371677)the High-Tech R&D Program of China(2012AA101108)+2 种基金the Achievements Transformation Project of National Agricultural Science and Technology,China(2010276)the Research and Establishment of Modern Industrial Technology System for National Cotton,China(nycytx-06-09)the Natural Science Foundation of Henan Province,China(2010A210006)
文摘Segregation analysis of the mixed genetic model of major gene plus polygene was used to identify the major genes for cotton yield-related traits using six generations P1, P2, F1, B1, B2, and F2 generated from the cross of Baimian 1 x TM-1. In addition to boll size and seed index, the major genes for the other five traits were detected： one each for seed yield, lint percentage, boll number, lint index; and two for lint yield. Quantitative trait locus/loci （QTL） mapping was performed in the F2 and F2：3 populations of above cross through molecular marker technology, and a total of 50 QTL （26 suggestive and 24 significant） for yield-related traits were detected. Four common QTL were discovered： qLP-3b（F2）/qLP-3（F2：3） and qLP-19b （F2）/qLP-19（F2：3） for lint percentage, qBN-17（F2）/qBN-17（F2：3） for boll number, and qBS-26b（F2）/qBS-26（F2：3） for boll size. Especially, qLP- 3b（Fz）/qLP-3（F2：3）, not only had LOD scores 〉3 but also exceeded the permutation threshold （5.13 and 5.29, respectively）, correspondingly explaining 23.47 and 29.55% of phenotypic variation. This QTL should be considered preferentially in marker assisted selection （MAS）. Segregation analysis and QTL mapping could mutually complement and verify, which provides a theoretical basis for genetic improvement of cotton yield-related traits by using major genes （QTL）.
基金supported by the National Natural Science Foundation of China(Grant Nos.31672170,31872950 and 31222048)the Natural Science Foundation of Shandong Province(Grant No.JQ201309),the Shandong“Double Tops”Program(Grant No.SYL2017YSTD06)the‘Taishan Scholar’Foundation of the People’s Government of Shandong Province(Grant No.ts20130932).
文摘To gain insight into the molecular and genetic basis of fruit size and shape in cucumber,we conducted Quantitative Trait Locus(QTL)mapping with F2 and BC1F1 populations derived froma cross between the Northern-China type inbred line CNS21 and the Southern-China type inbred line RNS7.Populations were evaluated during two developmental stages,ovary at anthesis and commercial fruit(immature fruit).A total of 13 major-effect QTLs(R2>10%)were detected for six traits,and one of them,fruit shape index 2.1,explained more than 50%of phenotypic variation.All QTLs distributed on chromosome(chr)1 and 2.We constructed a physical map containing almost all of the QTLs with their physical location from previous studies.For fruit size and shape,the highest number of QTLs were mapped on chr1 and chr6,and the fewest number were mapped on chr2 and chr7.At least one consensus region was presented on each chromosome.In addition,three candidate genes were predicted between the long-fruited and round-fruited inbred lines by comparing the sequences of the consensus region of chr3,where many QTLs for marketable fruit length had been detected.Our results provide a base for additional QTLs and molecular markers for fruit size and shape in cucumber breeding.
基金supported by the Project of the Changjiang Scholars and Innovative Research Team in University, the Ministry of Education of China (No.IRT0432)the 111 Project (No.B08025)
文摘Asiatic cotton （Gossypium arboreum L.） is an Old World cultivated cotton species. The sinense race was planted extensively in China. Due to the advances in spinning technology during the last century, the species was replaced by the New World allotetraploid cotton G. hirsutum L. Gossypium arboreum is still grown in India and Pakistan and also used as an elite in current cotton breeding programs. In addition, G. arboreum serves as a model for genomic research in Gossypium. In the present study, we generated an A-genome diploid cotton intraspecific genetic map including 264 SSR loci with three morphological markers mapped to 13 linkage groups. The map spans 2,508.71 cM with an average distance of 9.4 cM between adjacent loci. A population containing 176 F2：3 families was used to perform quantitative trait loci （QTL） mapping for 17 phenotypes using Multiple QTL Model （MQM） of MapQTL ver 5.0. Overall, 108 QTLs were detected on 13 chromosomes. Thirty-one QTLs for yield and its components were detected in the F2 population. Forty-one QTLs for yield and its components were detected in the F2：3 families with a total of 43 QTLs for fiber qualities. Two QTLs for seed cotton weight/plant and lint index and three QTLs for seed index were consistently detected both in F2 and F2：3. Most QTLs for fiber qualities and yields were located at the same interval or neighboring intervals. These results indicated that the negative correlation between fiber qualities and yield traits may result from either pleiotropic effect of one gene or linkage effects of multiple closely linked genes.
基金This research was supported by the Breeding New Varieties of Rice Suitable for Light and Simple Cultivation and Mechanized Production Project(2017YFD0100104)the Research and Development Plan for Key Areas in Guangdong Province(2018B020206002)+1 种基金the China Agriculture Research System(CARS-01-17)Special thanks are due to the South China Agricultural University Doctoral Innovative Talents(Domestic Training)Cultivation Program(CX2019N044)。
文摘Early seedling vigor(ESV)is a major breeding target in rice,especially under direct seeding.To identify quantitative trait locus(QTL)affecting ESV,a recombinant inbred line population derived from a cross between 02428 and YZX,two cultivars differing in vigor during early seedling growth,was used for QTL analysis.Nine traits associated with ESV were examined using a high-density map.Of 16 additive loci identified,three were detected in two generations and thus considered stable.Four epistatic interactions were detected,one of which was repeated in two generations.Further analysis of the pyramiding effect of the three stable QTL showed that the phenotypic value could be effectively improved with an increasing number of QTL.These results were combined with results from our previous QTL analysis of the germination index.The lines G58 and G182 combined all the favourable alleles of all three stable QTL for ESV and three QTL for germination speed.These two lines showed rapid germination and strong ESV.A total of 37 candidate differentially expressed genes were obtained from the regions of the three stable QTL by analysis of the dynamic transcriptomic expression profile during the seedling growth period of the two parents.The QTL are targets for ESV breeding and the candidate genes await functional validation.This study provides a theoretical basis and a genetic resource for the breeding of directseeded rice.
