Mapping and isolation of quantitative trait loci(QTLs)or genes controlling grain size or weight is very important to uncover the molecular mechanisms of seed development and crop breeding.To identify the QTLs controll...Mapping and isolation of quantitative trait loci(QTLs)or genes controlling grain size or weight is very important to uncover the molecular mechanisms of seed development and crop breeding.To identify the QTLs controlling grain size and weight,we developed a near isogenic line F_2(NIL-F_2)population,which was derived from a residual heterozygous plant in an F_7 generation of recombinant inbred line(RIL).With the completion of more than 30×whole genome re-sequencing of the parents,two DNA bulks for large and small grains,a total of 58.94 Gb clean nucleotide data were generated.A total of455 262 single nucleotide polymorphisms(SNPs)between the parents were identified to perform bulked QTL-seq.A candidate genomic region containing SNPs strongly associated with grain length and weight was identified from 15 to 20 Mb on chromosome 5.We designated the major QTL in the candidate region as q TGW5.3.Then,q TGW5.3 was further validated with PCR-based conventional QTL mapping method through developing simple sequence repeat and Insertion/Deletion markers in the F_2 population.Furthermore,recombinants and the progeny tests delimited the candidate region of q TGW5.3 to 1.13 Mb,flanked by HX5009(15.15 Mb)and HX5003(16.28 Mb).A set of NILs,selected from the F_2 population,was developed to evaluate the genetic effect of q TGW5.3.Significant QTL effects were detected on grain length,grain width and 1000-grain weight of H12-29 allele with 1.14 mm,-0.11 mm and 3.11 g,which explained 99.64%,95.51%and 97.32%of the phenotypic variations,respectively.展开更多
Seedlessness in grape(Vitis vinifera)is an important commercial trait for both the fresh and drying markets.However,despite numerous studies,the mechanisms and key genes regulating grape seedlessness are mostly unknow...Seedlessness in grape(Vitis vinifera)is an important commercial trait for both the fresh and drying markets.However,despite numerous studies,the mechanisms and key genes regulating grape seedlessness are mostly unknown.In this study,we sequenced the genomes of the V.vinifera seeded cultivar‘Red Globe’,the seedless cultivar‘Centennial Seedless’,and the derived hybrids.Nonsynonymous single nucleotide polymorphisms(SNPs)were identified by genome sequencing and analyzed using published transcriptome data.Nonsynonymous SNPs occurred in genes related to seed development,which were identified as protein kinases,transcription factors,and cytochrome P450 s and showed differential expression during ovule development in both seeded and seedless grapes.These nonsynonymous SNP-associated genes were mainly involved in biological processes such as hormone balance,seed coat and endosperm development,reproductive organ development,oxidation and reduction,senescence and cell death.A potential quantitative trait locus(QTL)region associated with seed size was characterized based on the SNP-index,and expression analysis of candidate genes in the QTL region during ovule development in multiple seeded and seedless grape cultivars were conducted.Three SNPs were further subjected to SNa Pshot analysis and one SNP in G8 showed 67.5%efficiency in the grape progeny validation.Overall,the data obtained in this study shed light on the differences in seed development between seeded and seedless progeny at the genomic level,which provides valuable resources for future functional studies and grape breeding.展开更多
Cold stress is a major problem in rice production. To rapidly identify genes for cold tolerance in Dongxiang wild rice（DWR, Oryza rufipogon Griff.）, sequencing-based bulked segregant analysis of QTL-seq method was u...Cold stress is a major problem in rice production. To rapidly identify genes for cold tolerance in Dongxiang wild rice（DWR, Oryza rufipogon Griff.）, sequencing-based bulked segregant analysis of QTL-seq method was used to resequence the extremely resistant（R） and susceptible（S） bulks of a backcross inbred lines（BILs） population（derived from Oryza sativa×O. rufipogon） and their parents. Single nucleotide polymorphisms（SNP）-index graphs and corresponding Δ（SNPindex） graphs（at 99 and 95% confidence levels） for R-and S-bulks detected a total of 2 609 candidate SNPs, including 58 candidate cold-tolerance genes. Quantitative real-time PCR analysis revealed that 5 out of the 58 candidate genes had significant differences in expression between O. sativa and O. rufipogon. Structural variation and functional annotations of the 5 candidate genes were also analyzed, and allowed us to identify 2 insertion-deletion（InDel） markers（12-7 and 12-16） that were linked with candidate genes on chromosome 12 in DWR. These results are helpful for cloning and using cold tolerance genes from common wild rice in cultivated rice.展开更多
为了分析樱桃番茄‘VFNT Cherry’(syn.LA1221)和加工番茄‘Heinz1706’组配的F1代果实质量超亲杂种优势的遗传基础,利用其F2群体,通过QTL-seq和单标记分析法进行了果实质量QTL定位,共检测到10个果实质量位点,其中8个位点的大果等位基...为了分析樱桃番茄‘VFNT Cherry’(syn.LA1221)和加工番茄‘Heinz1706’组配的F1代果实质量超亲杂种优势的遗传基础,利用其F2群体,通过QTL-seq和单标记分析法进行了果实质量QTL定位,共检测到10个果实质量位点,其中8个位点的大果等位基因为显性,包括部分显性位点5个[QTL for Fruit Weight 2.1(qFW2.1)、qFW5.2、qFW7.1、qFW8.1、qFW9.1]和超显性位点3个(qFW1.1、qFW5.1、qFW6.1)。而且qFW2.1、qFW5.1、qFW7.1、qFW8.1、qFW9.1的大果等位基因来自‘Heinz1706’,qFW1.1、qFW5.2、qFW6.1的大果等位基因来自‘VFNTCherry’。因此F1代番茄果实质量出现超亲现象可能是由于其聚合了来自双亲的显性大果等位基因。上述8个显性位点中qFW9.1的表型变异贡献率最高,达到12.19%。通过交换单株后代鉴定进一步验证了qFW9.1位点并将其定位区间缩小到4.5 Mb。展开更多
Stigma exsertion in male sterile lines of hybrid rice is important for seed yield.In the present study, ZS616 [Oryza sativa subsp.Xian(indica)], a male sterile line with a stigma exsertion rate(SER) as high as 94.5%, ...Stigma exsertion in male sterile lines of hybrid rice is important for seed yield.In the present study, ZS616 [Oryza sativa subsp.Xian(indica)], a male sterile line with a stigma exsertion rate(SER) as high as 94.5%, was crossed to DS552, a japonica line with almost no exserted stigmas.F3 plants with extremely low and high SER were sequenced to identify SER-associated quantitative trait loci(QTL).A major QTL for SER, qSER-3.1, was identified along with other QTL on chromosome 3 in a 3.9 Mb region.A total of 307 nonsynonymous single-nucleotide polymorphisms(SNPs) and 27 frame-shift insertion/deletions(InDels)differentiating ZS616 and DS552 were identified in the region containing qSER-3.1.Most SNPs(294) and InDels(25) were excluded after further analysis because they were shared by ZS616 and low(<2.0%) SER accessions in the Huazhong Agricultural University(HAU) core rice collection.Association analysis using the full HAU collection identified a 17-bp InDel in OS03 G0689400 as the most likely causal genetic variant underlying qSER-3.1.ZS616-type accessions(n = 54, with the 17-bp insertion) in the HAU collection had minimum(16.5%)and mean(39.6%) SERs significantly greater than those(n = 424) without the insertion(with minimum and mean SERs of 0.2% and 20.6%, respectively).Thus, this study identified a major QTL for stigma exsertion and revealed the mutation in a candidate gene for the QTL.展开更多
基金supported by National Natural Science Foundation of China(Grant No.31371605)Chinese High-Yielding Transgenic Program(Grant No.2016ZX08001-004)
文摘Mapping and isolation of quantitative trait loci(QTLs)or genes controlling grain size or weight is very important to uncover the molecular mechanisms of seed development and crop breeding.To identify the QTLs controlling grain size and weight,we developed a near isogenic line F_2(NIL-F_2)population,which was derived from a residual heterozygous plant in an F_7 generation of recombinant inbred line(RIL).With the completion of more than 30×whole genome re-sequencing of the parents,two DNA bulks for large and small grains,a total of 58.94 Gb clean nucleotide data were generated.A total of455 262 single nucleotide polymorphisms(SNPs)between the parents were identified to perform bulked QTL-seq.A candidate genomic region containing SNPs strongly associated with grain length and weight was identified from 15 to 20 Mb on chromosome 5.We designated the major QTL in the candidate region as q TGW5.3.Then,q TGW5.3 was further validated with PCR-based conventional QTL mapping method through developing simple sequence repeat and Insertion/Deletion markers in the F_2 population.Furthermore,recombinants and the progeny tests delimited the candidate region of q TGW5.3 to 1.13 Mb,flanked by HX5009(15.15 Mb)and HX5003(16.28 Mb).A set of NILs,selected from the F_2 population,was developed to evaluate the genetic effect of q TGW5.3.Significant QTL effects were detected on grain length,grain width and 1000-grain weight of H12-29 allele with 1.14 mm,-0.11 mm and 3.11 g,which explained 99.64%,95.51%and 97.32%of the phenotypic variations,respectively.
基金supported by the National Natural Science Foundation of China (U1603234)the Program for Innovative Research Team of Grape Germplasm Resources and Breeding of Shaanxi, China (2013KCT25)+2 种基金the Chinese Universities Scientific Fund (Z109021571 and 2452019170)the Natural Science Foundation of Hebei, China (C2021204146)the Scientific Research Program of Hebei Educational Commission, China (QN2020232)
文摘Seedlessness in grape(Vitis vinifera)is an important commercial trait for both the fresh and drying markets.However,despite numerous studies,the mechanisms and key genes regulating grape seedlessness are mostly unknown.In this study,we sequenced the genomes of the V.vinifera seeded cultivar‘Red Globe’,the seedless cultivar‘Centennial Seedless’,and the derived hybrids.Nonsynonymous single nucleotide polymorphisms(SNPs)were identified by genome sequencing and analyzed using published transcriptome data.Nonsynonymous SNPs occurred in genes related to seed development,which were identified as protein kinases,transcription factors,and cytochrome P450 s and showed differential expression during ovule development in both seeded and seedless grapes.These nonsynonymous SNP-associated genes were mainly involved in biological processes such as hormone balance,seed coat and endosperm development,reproductive organ development,oxidation and reduction,senescence and cell death.A potential quantitative trait locus(QTL)region associated with seed size was characterized based on the SNP-index,and expression analysis of candidate genes in the QTL region during ovule development in multiple seeded and seedless grape cultivars were conducted.Three SNPs were further subjected to SNa Pshot analysis and one SNP in G8 showed 67.5%efficiency in the grape progeny validation.Overall,the data obtained in this study shed light on the differences in seed development between seeded and seedless progeny at the genomic level,which provides valuable resources for future functional studies and grape breeding.
基金partially supported by the National Natural Science Foundation of China (31260255, 31360147 and 31660384)the Natural Science Foundation of Jiangxi Province, China (20151BAB204008)+1 种基金the Scientific Planning Project of Jiangxi Provincial Education Department, China (GJJ12184 and KJLD12059)the Major Projects in Jiangxi Province, China (20161ACF60022)
文摘Cold stress is a major problem in rice production. To rapidly identify genes for cold tolerance in Dongxiang wild rice（DWR, Oryza rufipogon Griff.）, sequencing-based bulked segregant analysis of QTL-seq method was used to resequence the extremely resistant（R） and susceptible（S） bulks of a backcross inbred lines（BILs） population（derived from Oryza sativa×O. rufipogon） and their parents. Single nucleotide polymorphisms（SNP）-index graphs and corresponding Δ（SNPindex） graphs（at 99 and 95% confidence levels） for R-and S-bulks detected a total of 2 609 candidate SNPs, including 58 candidate cold-tolerance genes. Quantitative real-time PCR analysis revealed that 5 out of the 58 candidate genes had significant differences in expression between O. sativa and O. rufipogon. Structural variation and functional annotations of the 5 candidate genes were also analyzed, and allowed us to identify 2 insertion-deletion（InDel） markers（12-7 and 12-16） that were linked with candidate genes on chromosome 12 in DWR. These results are helpful for cloning and using cold tolerance genes from common wild rice in cultivated rice.
文摘为了分析樱桃番茄‘VFNT Cherry’(syn.LA1221)和加工番茄‘Heinz1706’组配的F1代果实质量超亲杂种优势的遗传基础,利用其F2群体,通过QTL-seq和单标记分析法进行了果实质量QTL定位,共检测到10个果实质量位点,其中8个位点的大果等位基因为显性,包括部分显性位点5个[QTL for Fruit Weight 2.1(qFW2.1)、qFW5.2、qFW7.1、qFW8.1、qFW9.1]和超显性位点3个(qFW1.1、qFW5.1、qFW6.1)。而且qFW2.1、qFW5.1、qFW7.1、qFW8.1、qFW9.1的大果等位基因来自‘Heinz1706’,qFW1.1、qFW5.2、qFW6.1的大果等位基因来自‘VFNTCherry’。因此F1代番茄果实质量出现超亲现象可能是由于其聚合了来自双亲的显性大果等位基因。上述8个显性位点中qFW9.1的表型变异贡献率最高,达到12.19%。通过交换单株后代鉴定进一步验证了qFW9.1位点并将其定位区间缩小到4.5 Mb。
基金supported by the Zhejiang Provincial S&T Project on Breeding of Agricultural (Food) Crops (2016C020502)the Major Science and Technology Innovation Program of Hangzhou, China (2015012A09)
文摘Stigma exsertion in male sterile lines of hybrid rice is important for seed yield.In the present study, ZS616 [Oryza sativa subsp.Xian(indica)], a male sterile line with a stigma exsertion rate(SER) as high as 94.5%, was crossed to DS552, a japonica line with almost no exserted stigmas.F3 plants with extremely low and high SER were sequenced to identify SER-associated quantitative trait loci(QTL).A major QTL for SER, qSER-3.1, was identified along with other QTL on chromosome 3 in a 3.9 Mb region.A total of 307 nonsynonymous single-nucleotide polymorphisms(SNPs) and 27 frame-shift insertion/deletions(InDels)differentiating ZS616 and DS552 were identified in the region containing qSER-3.1.Most SNPs(294) and InDels(25) were excluded after further analysis because they were shared by ZS616 and low(<2.0%) SER accessions in the Huazhong Agricultural University(HAU) core rice collection.Association analysis using the full HAU collection identified a 17-bp InDel in OS03 G0689400 as the most likely causal genetic variant underlying qSER-3.1.ZS616-type accessions(n = 54, with the 17-bp insertion) in the HAU collection had minimum(16.5%)and mean(39.6%) SERs significantly greater than those(n = 424) without the insertion(with minimum and mean SERs of 0.2% and 20.6%, respectively).Thus, this study identified a major QTL for stigma exsertion and revealed the mutation in a candidate gene for the QTL.
