Genome-wide QTL mapping of yield and agronomic traits in two widely adapted winter wheat cultivars from multiple mega-environments

Authors: DHAKAL, SMIT - Texas Agrilife Research; LIU, XIAOXIAO - Texas Agrilife Research; Chu, Chenggen; RUDD, JACKIE - Texas Agrilife Research; IBRAHIM, AMIR - West Texas A & M University; XUE, QINGWU - Texas Agrilife Research; DEVKOTA, RAVINDRA - Texas Agrilife Research; BAKER, JASON - Texas Agrilife Research; BAKER, SHANNON - Texas Agrilife Research; BRYAN, SIMONEAUX - West Texas A & M University; GIGI, OPENA - West Texas A & M University; JESSUP, KIRK - Texas Agrilife Research; WANG, SHICHEN - Texas Agrilife Research; JOHNSON, CHARLES - Texas Agrilife Research; METZ, RICHARD - Texas Agrilife Research; LIU, SHUYU - West Texas A & M University

Submitted to: PeerJ
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/29/2021
Publication Date: 11/24/2021
Citation: Dhakal, S., Liu, X., Chu, C.N., Rudd, J.C., Ibrahim, A.M., Xue, Q., Devkota, R., Baker, J., Baker, S., Bryan, S., Gigi, O., Jessup, K.E., Wang, S., Johnson, C.D., Metz, R., Liu, S. 2021. Genome-wide QTL mapping of yield and agronomic traits in two widely adapted winter wheat cultivars from multiple mega-environments. PeerJ. 9. Article e12350. https://doi.org/10.7717/peerj.12350.
DOI: https://doi.org/10.7717/peerj.12350

Interpretive Summary: Improving crop yield is one of the major breeding goals. Understanding the genetic control of yield in varieties having high yield potential and identification of yield-associated regions in the genome will direct the efficient accumulation of favorable genes for yield to develop new varieties. In this study, yield trials in a set of wheat lines derived from a cross between two high-yielding varieties were conducted at different locations with varied level of irrigation managements across multiple years. Analyses using yield data and genetic information of those lines revealed many genes from the two parents were consistently affecting wheat grain yield and yield-related traits such as plant height, time to flowering and seed density under diverse environments. This research thus provided critical information for accurately tracking beneficial genes derived from the two high-yielding varieties, efficiently selecting high-yielding lines from their derivatives, and accelerating the process of new variety development.

Technical Abstract: Quantitative trait loci (QTL) analysis dissects complex traits through discerning their genetic control and genotype-by-environment interactions, and ultimately aids in marker development for marker-assisted breeding selection. A mapping population of 124 F5:7 recombinant inbred lines derived from the cross of ‘TAM 112’ / ‘TAM 111’ was grown under 28 diverse environments and evaluated for grain yield, test weight, heading date, and plant height. The objective of this study was to detect QTL conferring grain yield and agronomic traits in this population. Through a linkage map constructed using 5,948 single nucleotide polymorphisms (SNPs), 51 QTL were consistently identified in two or more environments. Ten QTL linked to two or more traits were also identified on chromosomes 1A, 1D, 4B, 4D, 6A, 7B, and 7D. Those QTL explained up to 31.9% of phenotypic variations with logarithm of odds (LOD) scores up to 64.9. Favorable alleles derived from TAM 111 had the potential of increasing yield and test weight up to 37.4 kg m-3 whereas those from TAM 112 showed the increase of 16.6 kg m-3. This study unveiled previously identified loci at major genes as well as new QTL and the favorable alleles for improving grain yield and agronomic traits.