Guanghui Chen, Li Sheng, Lijun Wu, Liang Yin, Shuangling Li, Hongfeng Wang, Xiao Jiang, Heng Wang, Yanmao Shi, Fudong Zhan, Xiaoyuan Chi, Chunjuan Qu, Yan Ren, Mei Yuan
{"title":"通过 SNP 阵列和 QTL-seq 鉴定花生抗晚期叶斑病的新型 QTLs","authors":"Guanghui Chen, Li Sheng, Lijun Wu, Liang Yin, Shuangling Li, Hongfeng Wang, Xiao Jiang, Heng Wang, Yanmao Shi, Fudong Zhan, Xiaoyuan Chi, Chunjuan Qu, Yan Ren, Mei Yuan","doi":"10.1016/j.jia.2024.03.008","DOIUrl":null,"url":null,"abstract":"Late leaf spot (LLS) is one of important diseases that causes severe yield losses in peanut. Peanut has various sources of resistance to LLS, and the identification of resistant QTLs and the development of related molecular markers are of great importance for breeding of LLS-resistant peanut. In this study, 173 individual lines of a recombinant inbred line (RIL) population and 48K SNP array for genotyping were used to construct a high-density genetic map with 1475 SNP marker and 20 linkage groups. A total of 11 QTLs were obtained through QTL analysis using the constructed genetic map. Among them, a stable major QTL . was identified on linkage group 2 in all six environments, with a phenotypic variation explained (PVE) ranging from 15.57 to 31.09%. Additionally, QTL-seq technology was also employed for QTL analysis of LLS resistance. As a result, 14 QTL loci related to LLS resistance were identified using the G prime algorithm. Notably, physical position of are coincided with that of . and . respectively. Gene annotation analysis within the 14 QTL intervals by QTL-seq revealed that there were a total of 163 NBS-LRR disease resistance genes, accounting for 22.86% of all R genes in peanut genome and showing a 4.26-fold enrichment with a p-value of 5.19e-57. Within the QTL region of the resistant parent Mi-2, there was a 5 Mb structural variation interval (SV) containing 81 NBS-LRR genes. A PCR diagnostic marker was developed, and validation data suggest that this SV might lead to gene deletion or replacement with other genes. This SV has the potential to enhance peanut resistance to late leaf spot disease. This study holds significant implications for improving peanut breeding for LLS resistance through development of associated molecular markers.","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":"20 1","pages":""},"PeriodicalIF":4.6000,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Identification of novel QTLs for resistance to late leaf spot in peanut by SNP array and QTL-seq\",\"authors\":\"Guanghui Chen, Li Sheng, Lijun Wu, Liang Yin, Shuangling Li, Hongfeng Wang, Xiao Jiang, Heng Wang, Yanmao Shi, Fudong Zhan, Xiaoyuan Chi, Chunjuan Qu, Yan Ren, Mei Yuan\",\"doi\":\"10.1016/j.jia.2024.03.008\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Late leaf spot (LLS) is one of important diseases that causes severe yield losses in peanut. Peanut has various sources of resistance to LLS, and the identification of resistant QTLs and the development of related molecular markers are of great importance for breeding of LLS-resistant peanut. In this study, 173 individual lines of a recombinant inbred line (RIL) population and 48K SNP array for genotyping were used to construct a high-density genetic map with 1475 SNP marker and 20 linkage groups. A total of 11 QTLs were obtained through QTL analysis using the constructed genetic map. Among them, a stable major QTL . was identified on linkage group 2 in all six environments, with a phenotypic variation explained (PVE) ranging from 15.57 to 31.09%. Additionally, QTL-seq technology was also employed for QTL analysis of LLS resistance. As a result, 14 QTL loci related to LLS resistance were identified using the G prime algorithm. Notably, physical position of are coincided with that of . and . respectively. Gene annotation analysis within the 14 QTL intervals by QTL-seq revealed that there were a total of 163 NBS-LRR disease resistance genes, accounting for 22.86% of all R genes in peanut genome and showing a 4.26-fold enrichment with a p-value of 5.19e-57. Within the QTL region of the resistant parent Mi-2, there was a 5 Mb structural variation interval (SV) containing 81 NBS-LRR genes. A PCR diagnostic marker was developed, and validation data suggest that this SV might lead to gene deletion or replacement with other genes. This SV has the potential to enhance peanut resistance to late leaf spot disease. 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Identification of novel QTLs for resistance to late leaf spot in peanut by SNP array and QTL-seq
Late leaf spot (LLS) is one of important diseases that causes severe yield losses in peanut. Peanut has various sources of resistance to LLS, and the identification of resistant QTLs and the development of related molecular markers are of great importance for breeding of LLS-resistant peanut. In this study, 173 individual lines of a recombinant inbred line (RIL) population and 48K SNP array for genotyping were used to construct a high-density genetic map with 1475 SNP marker and 20 linkage groups. A total of 11 QTLs were obtained through QTL analysis using the constructed genetic map. Among them, a stable major QTL . was identified on linkage group 2 in all six environments, with a phenotypic variation explained (PVE) ranging from 15.57 to 31.09%. Additionally, QTL-seq technology was also employed for QTL analysis of LLS resistance. As a result, 14 QTL loci related to LLS resistance were identified using the G prime algorithm. Notably, physical position of are coincided with that of . and . respectively. Gene annotation analysis within the 14 QTL intervals by QTL-seq revealed that there were a total of 163 NBS-LRR disease resistance genes, accounting for 22.86% of all R genes in peanut genome and showing a 4.26-fold enrichment with a p-value of 5.19e-57. Within the QTL region of the resistant parent Mi-2, there was a 5 Mb structural variation interval (SV) containing 81 NBS-LRR genes. A PCR diagnostic marker was developed, and validation data suggest that this SV might lead to gene deletion or replacement with other genes. This SV has the potential to enhance peanut resistance to late leaf spot disease. This study holds significant implications for improving peanut breeding for LLS resistance through development of associated molecular markers.
期刊介绍:
Journal of Integrative Agriculture publishes manuscripts in the categories of Commentary, Review, Research Article, Letter and Short Communication, focusing on the core subjects: Crop Genetics & Breeding, Germplasm Resources, Physiology, Biochemistry, Cultivation, Tillage, Plant Protection, Animal Science, Veterinary Science, Soil and Fertilization, Irrigation, Plant Nutrition, Agro-Environment & Ecology, Bio-material and Bio-energy, Food Science, Agricultural Economics and Management, Agricultural Information Science.