Late leaf spot disease(LLS)is one of the most important diseases that cause severe yield losses in peanut.Peanut has various sources of resistance to LLS,so the identification of resistant quantitative trait loci(QTLs...Late leaf spot disease(LLS)is one of the most important diseases that cause severe yield losses in peanut.Peanut has various sources of resistance to LLS,so the identification of resistant quantitative trait loci(QTLs)and the development of related molecular markers are of great importance for the breeding of LLS-resistant peanut.In this study,173 individual lines of a recombinant inbred line(RIL)population and the 48K SNP array for genotyping were used to construct a high-density genetic map with 1,475 bin markers and 20 linkage groups.A total of 11 QTLs were obtained through QTL analysis using the constructed genetic map.Among them,the stable major QTL qLLS.LG02 was identified on linkage group 2 in all six environments,with the phenotypic variation explained(PVE)ranging from 15.57 to 31.09%.QTL-seq technology was also employed for a QTL analysis of LLS resistance.As a result,14 QTL loci related to LLS resistance were identified using the G prime algorithm.Notably,the physical positions of qLLS02 and qLLS03 coincided with those of qLLS.LG02 and qLLS.LG03,respectively.Gene annotation analysis within the 14 QTL intervals from QTL-seq revealed a total of 163 nucleotide-binding site-leucine-rich repeat(NBS-LRR)disease resistance genes,accounting for 22.86%of all resistance(R)genes in the peanut genome and showing a 4.26-fold enrichment with a P-value of 5.19e-57.Within the QTL region qLLS02 of the resistant parent Mi-2,there was a 5 Mb structural variation(SV)interval containing 81 NBS-LRR genes.A PCR diagnostic marker was developed,and validation data suggested that this SV might lead to gene deletion or replacement with other genes.This SV has the potential to enhance peanut resistance to LLS.The results of this study have significant implications for improving peanut breeding for LLS resistance through the development of associated molecular markers.展开更多
Extremely high temperatures resulting from climate change have become a major challenge for increasing rice production.Therefore,our objective was to develop heat-tolerant aromatic rice varieties using the pedigree me...Extremely high temperatures resulting from climate change have become a major challenge for increasing rice production.Therefore,our objective was to develop heat-tolerant aromatic rice varieties using the pedigree method,focusing on selecting for seed-setting ability under extremely high temperatures along with the use of single nucleotide polymorphism/insertion and deletion(SNP/InDel)markers to improve aromatic properties and grain quality.Furthermore,the QTL-seq approach was utilized to identify QTLs for seed-setting rate in an F2 population subjected to heat stress.The candidate QTL regions were then aligned to confirm SNPs/InDels in synonymous F7 candidate heat-tolerant lines.The results revealed that four promising lines,namely 84-7-1-9,84-7-1-10,159-3-3-1,and 159-3-3-10,were classified as heat-tolerant with low amylose content.In addition,lines 84-7-1-9 and 84-7-1-10 were identified as aromatic rice encompassing the aroma gene(badh2).Regarding the QTL-seq results,the qSF2.1 region ranged from 311051 to 3929422 bp on chromosome 2,was identified based on the highest contrasting SNP index between the heat-susceptible and tolerant bulks.The candidate genes within this region include two genes related to heat shock proteins,three genes associated with pollen fertility,and four genes involved in heat stress and other abiotic stress responses.These genes are proposed as potential candidates for heat tolerance and could serve as targets in rice breeding programs aimed at enhancing heat tolerance.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
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
辣椒红色素是目前全球销量最大的纯天然可食用色素,培育高辣椒红色素品种为辣椒产业重要任务。通过对255份一年生栽培种辣椒核心种质的辣椒红素含量进行全基因组关联分析(genome-wide association study,GWAS),在第1、2、3、5、6、8、9...辣椒红色素是目前全球销量最大的纯天然可食用色素,培育高辣椒红色素品种为辣椒产业重要任务。通过对255份一年生栽培种辣椒核心种质的辣椒红素含量进行全基因组关联分析(genome-wide association study,GWAS),在第1、2、3、5、6、8、9、10、11和12号染色体均关联到与辣椒红素含量显著相关的区间,关联区间内共包括93个基因,根据功能注释和转录表达数据预测了3个影响辣椒果实中辣椒红素含量的候选基因。通过对高辣椒红色素材料Pep-340、低辣椒红色素材料Pep-276构建的F2群体进行混合分组分析法-测序(bulked segregant analysis-sequencing,BSA-seq)分析,在第1、3、5和10号染色体定位到与辣椒红色素含量相关区间,其中第3和5号染色体上的定位区间与GWAS分析中的显著相关区间相近或重合;利用这两个区间的In Del分子标记,进行遗传连锁分析,将调控辣椒红色素含量基因定位在3号染色体的q CC3.1,物理位置为22.8~25.9 Mb,其中含有99个基因,根据功能注释和转录组分析,预测了4个影响辣椒果实中辣椒红色素含量的候选基因Capana03g001314、Capana03g001325、Capana03g001334和Capana03g001387。研究结果为调控辣椒中辣椒红色素含量基因精细定位及分子标记辅助选择育种奠定基础。展开更多
基金funded by the Key Research and Development Program of Shandong Province,China(2022LZGC007 and 2018GNC110036)the Natural Science Foundation of Shandong Province,China(ZR2024MC038 and ZR2020QC121)+5 种基金the Taishan Scholar Project Funding,China(tsqn201812121)the Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences,China(CXGC2024G20,CXGC2023A06,CXGC2022A03,and CXGC2022F33)the Science and Technology for People’s Livelihood Project of Qingdao,China(20-3-4-26-nsh)the China Agriculture Research System(CARS-13)the National Natural Science Foundation of China(32072107)the Major Scientific and Technological Project in Xinjiang,China(2022A02008-3).
文摘Late leaf spot disease(LLS)is one of the most important diseases that cause severe yield losses in peanut.Peanut has various sources of resistance to LLS,so the identification of resistant quantitative trait loci(QTLs)and the development of related molecular markers are of great importance for the breeding of LLS-resistant peanut.In this study,173 individual lines of a recombinant inbred line(RIL)population and the 48K SNP array for genotyping were used to construct a high-density genetic map with 1,475 bin markers and 20 linkage groups.A total of 11 QTLs were obtained through QTL analysis using the constructed genetic map.Among them,the stable major QTL qLLS.LG02 was identified on linkage group 2 in all six environments,with the phenotypic variation explained(PVE)ranging from 15.57 to 31.09%.QTL-seq technology was also employed for a QTL analysis of LLS resistance.As a result,14 QTL loci related to LLS resistance were identified using the G prime algorithm.Notably,the physical positions of qLLS02 and qLLS03 coincided with those of qLLS.LG02 and qLLS.LG03,respectively.Gene annotation analysis within the 14 QTL intervals from QTL-seq revealed a total of 163 nucleotide-binding site-leucine-rich repeat(NBS-LRR)disease resistance genes,accounting for 22.86%of all resistance(R)genes in the peanut genome and showing a 4.26-fold enrichment with a P-value of 5.19e-57.Within the QTL region qLLS02 of the resistant parent Mi-2,there was a 5 Mb structural variation(SV)interval containing 81 NBS-LRR genes.A PCR diagnostic marker was developed,and validation data suggested that this SV might lead to gene deletion or replacement with other genes.This SV has the potential to enhance peanut resistance to LLS.The results of this study have significant implications for improving peanut breeding for LLS resistance through the development of associated molecular markers.
基金Agricultural Research Development Agency in Thailand for financing the study and the provision of this research.
文摘Extremely high temperatures resulting from climate change have become a major challenge for increasing rice production.Therefore,our objective was to develop heat-tolerant aromatic rice varieties using the pedigree method,focusing on selecting for seed-setting ability under extremely high temperatures along with the use of single nucleotide polymorphism/insertion and deletion(SNP/InDel)markers to improve aromatic properties and grain quality.Furthermore,the QTL-seq approach was utilized to identify QTLs for seed-setting rate in an F2 population subjected to heat stress.The candidate QTL regions were then aligned to confirm SNPs/InDels in synonymous F7 candidate heat-tolerant lines.The results revealed that four promising lines,namely 84-7-1-9,84-7-1-10,159-3-3-1,and 159-3-3-10,were classified as heat-tolerant with low amylose content.In addition,lines 84-7-1-9 and 84-7-1-10 were identified as aromatic rice encompassing the aroma gene(badh2).Regarding the QTL-seq results,the qSF2.1 region ranged from 311051 to 3929422 bp on chromosome 2,was identified based on the highest contrasting SNP index between the heat-susceptible and tolerant bulks.The candidate genes within this region include two genes related to heat shock proteins,three genes associated with pollen fertility,and four genes involved in heat stress and other abiotic stress responses.These genes are proposed as potential candidates for heat tolerance and could serve as targets in rice breeding programs aimed at enhancing heat tolerance.
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 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.
