Novel and favorable genomic regions for spike related traits in a wheat germplasm Pubing 3504 with high grain number per spike under varying environments

Grain number per spike (GNPS) is a major factor in wheat yield breeding. A new wheat germplasm Pubing 3504 shows superior features in spike traits. To elucidate the genetic basis of spike and yield related traits in Pubing 3504, 282 F2:3 families were generated from the cross Pubing 3504×Jing 4839, and seven spike and yield related traits, including GNPS, spike length (SL), kernel number per spikelet (KPS), spikelet number per spike (SNS), thousand-grain weight (TGW), spike number per plant (SNP), and plant height (HT) were investigated. Correlation analysis indicated significant positive correlations between GNPS and spike-related traits, including KPS, SNS, and SL, especially KPS. A genetic map was constructed using 190 polymorphic simple sequence repeat (SSR), expressed sequence tag (EST)-SSR, and sequence-tagged-site (STS) markers. For the seven traits measured, a total of 37 quantitative trait loci (QTLs) in a single-environment analysis and 25 QTLs in a joint-environment analysis were detected. Additive effects of 70.3% (in a single environment) and 57.6% (in a joint environment) of the QTLs were positively contributed by Pubing 3504 alleles. Five important genomic regions on chromosomes 1A, 4A, 4B, 2D, and 4D could be stably detected in different environments. Among these regions, the marker interval Xmag834–Xbarc83 on the short arm of chromosome 1A was a novel important genomic region that included QTLs controlling GNPS, KPS, SNS, TGW, and SNP with stable environmental repeatability. This genomic region can improve the spike trait and may play a key role in improving wheat yield in the future. We deduced that this genomic region was vital to the high GNPS of Pubing 3504.