Abstract
Fine mapping of quantitative trait loci (QTL) for spikelet number per spike (SNS) will facilitate gene cloning and genetic manipulation of SNS to increase grain yield. The present study developed 185 pairs of near-isogenic lines (NILs) using three heterozygous inbred families in a recombination inbred line population from a cross between UI Platinum (UIP) and SY Capstone (SYC). These NILs contain 185 unique recombination events for a SNS QTL, QfSNS.uia-5A, identified originally in a doubled haploid population derived from UIP x SYC. Using peak SNPs and promoter capture sequence data of the two parents, 16 Kompetitive allele-specific PCR (KASP) markers were developed and genotyped in the 185 NIL pairs. The SNS of 185 pairs of near-isogenic lines was assessed in four field experiments in two locations (Moscow and Aberdeen, ID) over two years (2020 and 2021). Through linking Student’s t-test results of SNS phenotypic data and KASP genotyping data, the QfSNS.uia-5A was fine-mapped from a 13 cM region to a 1.8 Mb region (643,622,710 bp - 645,468,705 bp, RefSeq v1.0). This region contains 52 annotated genes and two of them showed the highest expression in spike apical development stages compared to the cloned SNS-related genes involved in the AP2 regulated flowering pathway. The two genes were TraesCS5A02G468700 encoding a K-box domain protein and TraesCS5A02G468800 encoding an AP2/ERF domain-containing protein. The functional domain of TraesCS5A02G468800 is the same as genes Q and FRIZZY PANICLE, two cloned major SNS genes in wheat. TraesCS5A02G468700 was monomorphic, while TraesCS5A02G468800 was amplified in the two parents, UI Platinum and SY Capstone with three pairs of primers. Taken together, the TraesCS5A02G468800 is the most likely candidate gene for QfSNS.uia-5A among the 52 genes in the fine-mapping region. The candidate gene will be validated through transgenic and mutagenic approaches for loss-of-function and gain-of-function analysis in the future.