Genetic variations and epistatic interactions for agronomic and yield traits in winter wheat population derived from ‘TAM 204’ and ‘Iba’ cultivars

Authors: RAUF, YAHYA - Texas A&M University; ANTELO, VALENZUELA - Texas A&M University; DOGAN, MEHMET - Texas A&M University; Chu, Chenggen; BAKER, SHANNON - Texas A&M University; BAKER, JASON - Texas A&M University; HATHCOAT, DANIEL - Texas A&M University; OPENA, GERALDINE - Texas A&M University; XUE, QIGNWU - Texas A&M University; RUDD, JACKIE - Texas A&M University; IBRAHIM, AMIR - Texas A&M University; ZHANG, JUNLI - Texas A&M University; LIU, SHUYU - Texas A&M University

Submitted to: Agronomy Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/1/2026
Publication Date: 4/2/2026
Citation: Rauf, Y., Antelo, V., Dogan, M., Chu, C.N., Baker, S.A., Baker, J.A., Hathcoat, D., Opena, G., Xue, Q., Rudd, J., Ibrahim, A., Zhang, J., Liu, S. 2026. Genetic variations and epistatic interactions for agronomic and yield traits in winter wheat population derived from ‘TAM 204’ and ‘Iba’ cultivars. Agronomy Journal. 16(7):755. https://doi.org/10.3390/agronomy16070755.
DOI: https://doi.org/10.3390/agronomy16070755

Interpretive Summary: Improving grain yield in wheat remains a top priority. However, wheat yield is affected by both genetic factors and environmental conditions, and genetic control of the trait is complex and involves numerous genes. This study used a wheat population derived from the cross between two elite varieties and evaluated grain yield at several locations of the US Southern Great Plains under multiple years. Genetic studies identified many genomic regions affecting yield and yield-related agronomic traits with some regions showing consistent correlation more than one environment. A few yield-related genomic regions also affect heading time and grain weight, traits that are closely related to grain yield. Furthermore, interactions between genomic regions associated with yield were detected, demonstrating the complex genetic control of yield. Findings in this research revealed yield genetic variations in two superior wheat varieties, which provided useful information for recombination of favorable genetic variations to breed new high-yielding varieties.

Technical Abstract: Improving grain yield in wheat remains a top priority, re-quiring integrated breeding and genetic strategies. This complexity poses a major challenge, driven by quantitative polygenic inheritance, environmental influence, and intricate genetic interactions. We investigated genetic factors and their interactions for agronomic and yield traits in two high-yielding winter wheat cultivars adapted to the US Southern Great Plains. A bi-parental mapping population consisting of 221 F7 recombinant inbred lines (RIL) derived from ‘TAM 204’ and ‘Iba’ was evaluated for three years in 11 Texas environments. Both parents and RIL population were genotyped on Illumina NovaSeq 6000 and sequences were aligned to IWGSC RefSeq v1.0 using Bowtie2 for SNP calling. For QTL analyses, each trait was analyzed by individual environment, across multiple environments and mega environments. A total of 86 QTL were mapped for five traits and among them 32 were consistent in more than one environment or analysis. Among consistent QTL, four were pleiotropic to more than one agronomic or yield traits mapped on chromosomes 2B (57.18, 59.47 Mb) and 2D (29.34, 40.64 Mb). The consistent QTL on chromosome 2D (29.43 Mb) was pleiotropic to GYLD, DTH, TW and TKW and explained maximum phenotypic variation for all traits. Most likely this region represents photoperiod gene (Ppd-D1) in Iba. Another QTL on chromosome 2D (40.64 Mb) was pleiotropic to GYLD and TW and based on the physical position comparisons it likely reflects a unique locus in Iba. The pleiotropic consistent QTL Qgyld.tamu.2B.59 from TAM 204 represents Ppd-B1 gene. Moreover, it is more likely that Qdth.tamu.5B.575 represents the Vrn-B1 gene in Iba. A total of 23 digenic epistatic interactions involved consistent QTL for all traits. Amongst these, epistatic interactions between the consistent QTL on 2B (57.18 Mb) and 2D (29.34 Mb) were observed for GYLD, DTH and TKW. Our findings revealed key allelic diversity and interaction effects in elite wheat cultivars, paving the way for marker development for identified pleiotropic loci and implementation in marker-assisted selection and re-combination breeding.