QTL analysis of yield and end-use quality traits in Texas hard red winter wheat

Authors: DOGAN, MEHMET - Texas A&M Agrilife; WANG, ZHEN - Texas A&M Agrilife; CERIT, MUSTAFA - Texas A&M Agrilife; VALENZUELA-ANTELO, JORGE - Texas A&M Agrilife; DHAKAL, SMIT - Texas A&M Agrilife; CHU, CHENGGAN - US Department Of Agriculture (USDA); XUE, QINGWU - Texas A&M Agrilife; IBRAHIM, AMIR - Texas A&M University; RUDD, JACKIE - Texas A&M Agrilife; Bernardo, Amy; St Amand, Paul; Bai, Guihua; ZHANG, HONGBIN - Texas A&M Agrilife; LIU, SHUYU - Texas A&M Agrilife

Submitted to: Agronomy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/22/2023
Publication Date: 2/26/2023
Citation: Dogan, M., Wang, Z., Cerit, M., Valenzuela-Antelo, J., Dhakal, S., Chu, C., Xue, Q., Ibrahim, A., Rudd, J., Bernardo, A.E., St Amand, P.C., Bai, G., Zhang, H., Liu, S. 2023. QTL analysis of yield and end-use quality traits in Texas hard red winter wheat. Agronomy. Agronomy 13(3). Article 689. https://doi.org/10.3390/agronomy13030689.
DOI: https://doi.org/10.3390/agronomy13030689

Interpretive Summary: To identify the QTL linked to yield, its components, end-use quality traits under dryland and irrigated conditions, a QTL mapping study was conducted using a recombinant inbred line (RIL) population and linkage map of 2658 single nucleotide polymorphisms (SNPs). We mapped 14 consistent QTLs on 11 chromosomes with three potential novel QTLs on 1A, 3B and 6D. Six pleiotropic QTLs were identified on 5 chromosomes, and three of them were also consistent QTLs that were co-localized with known genes. The first QTL for dough mixing properties overlaps with Glu-D1, the second QTL for kernel-related traits was close to the TaCWI-4A (cell wall invertase) gene, and the third QTL was co-localized with the TaCWI-5D gene for kernel traits. These consistent and pleiotropic QTLs should be useful for improvement of end-use quality, yield, and other agronomic traits in wheat-breeding programs through marker-assisted selection.

Technical Abstract: Genetic dissection of complex traits by quantitative trait locus (QTL) analysis permits the understanding of the genotypic effects of QTL, interactions between QTLs, and QTL-by-environment interactions in wheat. This study aimed to identify the QTL linked to yield, its components, end-use quality traits including kernel, 'our, and dough rheology, and related agronomic traits under dryland and irrigated conditions. A mapping population of 179 F2:6 recombinant inbred lines (RILs) derived from ‘TAM 111’/‘TX05A001822’ was evaluated for these traits to investigate their genetic stability and phenotypic plasticity using 2658 single nucleotide polymorphisms (SNPs) with 35 linkage groups. Traits associated with chromosome regions were detected for individual and across-environment QTL by inclusive composite interval mapping. A total of 30 QTL regions were identi'ed, including 14 consistent QTLs mapped on 11 chromosomes and six pleiotropic QTLs mapped on 5 chromosomes. Three consistent QTLs in chromosomes 1A, 3B, and 6D might be novel. Three major QTLs with both consistent and pleiotropic effects were co-localized with known genes. The 'rst QTL for dough mixing properties was physically clustered around Glu-D1 and had an phenotypic variation explained (PVE) up to 31.3%. The second QTL for kernel-related traits was physically close to the TaCWI-4A (cell wall invertase) gene, which in'uences the thousand kernel weight, heading date, and harvest index, with a PVE of up to 12.3%. The third QTL, which was co-localized with the TaCWI-5D gene for kernel traits, was identi'ed with a PVE of 6.7%. Epistasis was also detected, but major QTLs were not involved in signi'cant epistasis or interactions with environmental effects. The current study provided new information that is useful for enhanced wheat breeding, which will bene't from the deployment of the favorable alleles for end-use quality, yield, and other agronomic traits in wheat-breeding programs through marker-assisted selection.