Identification and development of KASP markers for genetic loci controlling plant height in bread wheat and evaluation their effects using near isogenic lines

Abstract Background Plant height (PH), as a key trait of plant architecture, is the embodiment of biomass accumulation and plays a critical role in determining wheat yield. Excavating diverse PH genes and understanding their pleiotropic effects on important agronomic traits are essential to enrich the PH gene pool and facilitate their further application in breeding. Results In this study, five stable PH QTLs were identified on chromosome 2B, 4A, 4B, 5A and 6A in a double haploid (DH) population from the cross between two elite wheat cultivars, Chuanmai 42 and Kechengmai 1. The QPh.cib-4B and QPh.cib-6A were major QTL and had a significant additive effect on PH. The QPh.cib-4B was confirmed as the Rht-B1, and QPh.cib-6A might be a new QTL. The major QTLs were further validated in different genetic backgrounds using the Kompetitive Allele-Specific PCR (KASP) markers. Using near-isogenic lines (NILs), QPh.cib-6A was demonstrated to pleiotropically increase plant height (PH), thousand grain weight (TGW), and spike length (SL) without negatively affecting grain number per spike (GNS) or spikelet number per spike (SNS). In contrast, QPh.cib-4B exhibited significant effects on PH but had no influence on TGW, GNS, SL, or SNS. Notably, the frequency of elite haplotype of QPh.cib-6A remains relatively low in Chinese wheat varieties. Thus, the combination of QPh.cib-4B and QPh.cib-6A represents a promising genetic module with considerable potential for high-yield wheat breeding. Expression analysis in NILs and sequence characterization identified TraesCS6A02G234400 and TraesCS6A02G235300 as the candidate genes for QPh.cib-6A. Conclusions This study identified five QTLs for PH in wheat. Two major QTLs were further validated in different genetic backgrounds, and their genetic effects on yield-related traits were analyzed in near-isogenic lines (NILs) to evaluate their potential in wheat breeding. Taken together, our results advance our understanding of the genetic basis for PH and enrich the PH QTL pool. Clinical trial number Not applicable.