High resolution mapping of agro-morphological and grain traits in bread wheat using SNP-based QTL analysis

Abstract

Wheat (Triticum aestivum L.) is among the most extensively grown staple crops worldwide. A set of 188 recombinant inbred lines (RILs) derived from a cross between HD2932 and Synthetic 46 was evaluated over three consecutive years (2021–22, 2022–23, and 2023–24) for plant height (PH), spike length (SL), spikelets per spike (SPS), thousand kernel weight (TKW), kernel length (KL), kernel width (KW), and kernel thickness (KT). The population displayed wide phenotypic variability with quantitative inheritance for all the traits. High-density genotyping was performed using 910 SSR markers and a 35K SNP array. Twenty-eight QTLs, including six for PH, two for SL, three for SPS, two for TKW, five for KL, six for KW, and four for KT distributed across 16 chromosomes were identified. QTkw.iari_4B, flanked by Xgwm149–AX-94559916, was detected in all three environments (Q × E not formally tested) consistently and co-localized with QTLs for PH, KL, and KT, indicating a potentially important genomic region for yield improvement. Promising lines such as RIL 122 and RIL 66 exhibited superior kernel characteristics, while RIL 155 showed lower expression values. In silico analysis identified 28 candidate genes within these QTL regions, offering insights into trait regulation. These findings may serve as potential resources for marker-assisted selection in wheat breeding programs to enhance yield and grain quality parameters.