Genetic identification and characterization of a locus controlling productive tiller number with breeding value in Chinese endemic wheat.

This study identified and validated novel PTN QTL and predicted corresponding candidate genes, providing a genetic basis for the improvement of tiller number and grain yield in wheat. Productive tiller number (PTN) is a central component of wheat yield, yet its genetic regulation remains complex and highly responsive to environmental variation. This study employed a Chinese endemic wheat association population of 182 accessions to systematically dissect the genetic architecture of PTN across three environments. Phenotypic analysis revealed moderate-to-high genetic control (H2 = 69.59%) coupled with evident genotype-environment interactions. Genome-wide association mapping identified a major locus, QPTN.sicau-CEW-5D, which accounted for 70.6% of the significant associations and harbored four distinct haplotypes. The favorable Hap1 exhibited significantly higher PTN and plant height but with no significant differences on spike length and spikelet number per spike across multiple environments, suggesting its great potential in enhancing grain yield Validation in an independent population comprising 220 Sichuan wheat cultivars and landraces confirmed the highly significant and stable effect of QPTN.sicau-CEW-5D, in sharp contrast to the environment-dependent performance of loci on chromosomes 3A and 6A. Through candidate gene analysis integrating non-synonymous variant screening and independent association testing, we prioritized two receptor-like protein kinase (RLK) genes (TraesCS5D02G556900 and TraesCS5D02G557800) and one NLR gene (TraesCS5D02G557600) as key regulators of PTN variation. These findings provide novel insights into the genetic basis governing wheat tiller development and offer reliable genomic targets and superior haplotypes for marker-assisted breeding.