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Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study.
Theor Appl Genet. 2018 May; 131(5):1073-1090.TA

Abstract

KEY MESSAGE

Coincident regions on chromosome 4B for GW, on 5A for SD and TSS, and on 3A for SL and GNS were detected through an integration of a linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A and 6A were identified with high PVE% on a composite map. The panicle traits of wheat, such as grain number per spike and 1000-grain weight, are closely correlated with grain yield. Superior and effective alleles at loci related to panicles developments play a crucial role in the progress of molecular improvement in wheat yield breeding. Here, we revealed several notable allelic variations of seven panicle-related traits through an integration of genome-wide association mapping and a linkage analysis. The linkage analysis was performed using a recombinant inbred line (RIL) population (173 lines of F8:9) with a high-density genetic map constructed with 90K SNP arrays, Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) markers in five environments. Thirty-five additive quantitative trait loci (QTL) were discovered, including eleven stable QTLs on chromosomes 1A, 2D, 4B, 5B, 6B, and 6D. The marker interval between EX_C101685 and RAC875_C27536 on chromosome 4B exhibited pleiotropic effects for GW, SL, GNS, FSN, SSN, and TSS, with the phenotypic variation explained (PVE) ranging from 5.40 to 37.70%. In addition, an association analysis was conducted using a diverse panel of 205 elite wheat lines with a composite map (24,355 SNPs) based on the Illumina Infinium assay in four environments. A total of 73 significant marker-trait associations (MTAs) were detected for panicle traits, which were distributed across all wheat chromosomes except for 4D, 5D, and 6D. Consensus regions between RAC875_C27536_611 and Tdurum_contig4974_355 on chromosome 4B for GW in multiple environments, between QTSS5A.7-43 and BS00021805_51 on 5A for SD and TSS, and between QSD3A.2-164 and RAC875_c17479_359 on 3A for SL and GNS in multiple environments were detected through linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A, and 6A were identified with high PVE% on a composite map. This study provides potentially valuable information on the dissection of yield-component traits and valuable genetic alleles for molecular-design breeding or functional gene exploration.

Authors+Show Affiliations

State Key Laboratory of Crop Biology/Key Laboratory of Crop Water Physiology and Drought-Tolerance Germplasm Improvement, Ministry of Agriculture/Group of Wheat Quality Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.State Key Laboratory of Crop Biology/Key Laboratory of Crop Water Physiology and Drought-Tolerance Germplasm Improvement, Ministry of Agriculture/Group of Wheat Quality Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.State Key Laboratory of Crop Biology/Key Laboratory of Crop Water Physiology and Drought-Tolerance Germplasm Improvement, Ministry of Agriculture/Group of Wheat Quality Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.State Key Laboratory of Crop Biology/Key Laboratory of Crop Water Physiology and Drought-Tolerance Germplasm Improvement, Ministry of Agriculture/Group of Wheat Quality Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.State Key Laboratory of Crop Biology/Key Laboratory of Crop Water Physiology and Drought-Tolerance Germplasm Improvement, Ministry of Agriculture/Group of Wheat Quality Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.State Key Laboratory of Crop Biology/Key Laboratory of Crop Water Physiology and Drought-Tolerance Germplasm Improvement, Ministry of Agriculture/Group of Wheat Quality Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.State Key Laboratory of Crop Biology/Key Laboratory of Crop Water Physiology and Drought-Tolerance Germplasm Improvement, Ministry of Agriculture/Group of Wheat Quality Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.State Key Laboratory of Crop Biology/Key Laboratory of Crop Water Physiology and Drought-Tolerance Germplasm Improvement, Ministry of Agriculture/Group of Wheat Quality Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.State Key Laboratory of Crop Biology/Key Laboratory of Crop Water Physiology and Drought-Tolerance Germplasm Improvement, Ministry of Agriculture/Group of Wheat Quality Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, People's Republic of China. jctian9666@163.com.State Key Laboratory of Crop Biology/Key Laboratory of Crop Water Physiology and Drought-Tolerance Germplasm Improvement, Ministry of Agriculture/Group of Wheat Quality Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, People's Republic of China. cjs777777@126.com.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29470622

Citation

Liu, Kai, et al. "Genetic Dissection of Wheat Panicle Traits Using Linkage Analysis and a Genome-wide Association Study." TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, vol. 131, no. 5, 2018, pp. 1073-1090.
Liu K, Sun X, Ning T, et al. Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study. Theor Appl Genet. 2018;131(5):1073-1090.
Liu, K., Sun, X., Ning, T., Duan, X., Wang, Q., Liu, T., An, Y., Guan, X., Tian, J., & Chen, J. (2018). Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 131(5), 1073-1090. https://doi.org/10.1007/s00122-018-3059-9
Liu K, et al. Genetic Dissection of Wheat Panicle Traits Using Linkage Analysis and a Genome-wide Association Study. Theor Appl Genet. 2018;131(5):1073-1090. PubMed PMID: 29470622.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study. AU - Liu,Kai, AU - Sun,Xiaoxiao, AU - Ning,Tangyuan, AU - Duan,Xixian, AU - Wang,Qiaoling, AU - Liu,Tongtong, AU - An,Yuling, AU - Guan,Xin, AU - Tian,Jichun, AU - Chen,Jiansheng, Y1 - 2018/02/22/ PY - 2017/08/18/received PY - 2018/01/19/accepted PY - 2018/2/23/pubmed PY - 2018/4/24/medline PY - 2018/2/23/entrez SP - 1073 EP - 1090 JF - TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik JO - Theor Appl Genet VL - 131 IS - 5 N2 - KEY MESSAGE: Coincident regions on chromosome 4B for GW, on 5A for SD and TSS, and on 3A for SL and GNS were detected through an integration of a linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A and 6A were identified with high PVE% on a composite map. The panicle traits of wheat, such as grain number per spike and 1000-grain weight, are closely correlated with grain yield. Superior and effective alleles at loci related to panicles developments play a crucial role in the progress of molecular improvement in wheat yield breeding. Here, we revealed several notable allelic variations of seven panicle-related traits through an integration of genome-wide association mapping and a linkage analysis. The linkage analysis was performed using a recombinant inbred line (RIL) population (173 lines of F8:9) with a high-density genetic map constructed with 90K SNP arrays, Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) markers in five environments. Thirty-five additive quantitative trait loci (QTL) were discovered, including eleven stable QTLs on chromosomes 1A, 2D, 4B, 5B, 6B, and 6D. The marker interval between EX_C101685 and RAC875_C27536 on chromosome 4B exhibited pleiotropic effects for GW, SL, GNS, FSN, SSN, and TSS, with the phenotypic variation explained (PVE) ranging from 5.40 to 37.70%. In addition, an association analysis was conducted using a diverse panel of 205 elite wheat lines with a composite map (24,355 SNPs) based on the Illumina Infinium assay in four environments. A total of 73 significant marker-trait associations (MTAs) were detected for panicle traits, which were distributed across all wheat chromosomes except for 4D, 5D, and 6D. Consensus regions between RAC875_C27536_611 and Tdurum_contig4974_355 on chromosome 4B for GW in multiple environments, between QTSS5A.7-43 and BS00021805_51 on 5A for SD and TSS, and between QSD3A.2-164 and RAC875_c17479_359 on 3A for SL and GNS in multiple environments were detected through linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A, and 6A were identified with high PVE% on a composite map. This study provides potentially valuable information on the dissection of yield-component traits and valuable genetic alleles for molecular-design breeding or functional gene exploration. SN - 1432-2242 UR - https://www.unboundmedicine.com/medline/citation/29470622/Genetic_dissection_of_wheat_panicle_traits_using_linkage_analysis_and_a_genome_wide_association_study_ L2 - https://dx.doi.org/10.1007/s00122-018-3059-9 DB - PRIME DP - Unbound Medicine ER -