QTL detection, validation, candidate genes and KASP markers for pre-harvest sprouting tolerance in white grained common wheat

Authors: KUMAR, MANOJ - Chaudhary Charan Singh University; KUMAR, SACHIN - Chaudhary Charan Singh University; Kumar, Neeraj; SINGH, VIVUDH - Chaudhary Charan Singh University; SHARMA, HEMANT - Chaudhary Charan Singh University; KUMAR, SOURABH - Chaudhary Charan Singh University; BOATWRIGHT, LUCAS - Clemson University; KNOX, RON - Agriculture And Agri-Food Canada; JAISWAL, JAI - Govind Ballabh Pant University Of Agriculture And Technology; BALYAN, HARINDRA - Chaudhary Charan Singh University

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/24/2025
Publication Date: 11/13/2025
Citation: Kumar, M., Kumar, S., Kumar, N.N., Singh, V.P., Sharma, H., Kumar, S., Boatwright, L.J., Knox, R., Jaiswal, J.P., Balyan, H.S. 2025. QTL detection, validation, candidate genes and KASP markers for pre-harvest sprouting tolerance in white grained common wheat. BMC Plant Biology. 25:1558. https://doi.org/10.1186/s12870-025-07486-7.
DOI: https://doi.org/10.1186/s12870-025-07486-7

Interpretive Summary: Pre-harvest sprouting (PHS) is a problem in wheat that happens when it rains before harvest, causing the seeds to sprout early while they are still on the plant. This event lowers the grain yield and decreases quality which often leads to grain rejection at the grain market or processing mill. PHS is a quantitative trait controlled by many genes with small effects. To identify some of these small effects, we studied 386 wheat lines made from crossing two wheat parents with one that resists PHS (SC8021-V2) to another line (AC Karma). The progeny lines from this cross were grown at two different field locations in Northern India over two consecutive years. The study measured how much the seed sprouted (sprouting score) and how much sprouting affected the enzyme activity in the seed which is one of the key parameters of grain quality in wheat. It also looked at the DNA of the plants using a special tool with 90,000 DNA markers to find genes linked to PHS resistance traits. The tool found 29 gene regions (called QTLs) that affect PHS and grain quality related traits. Of these 29 regions, 16 were novel. In these regions, 368 genes were identified that are linked to hormones that control seed sprouting, seed protection and stress resistance. The 386 lines were checked for presence of the beneficial gene regions. In total, five lines carrying useful versions were selected in this study. Finally, three easy-to-use DNA markers were developed to help wheat breeders choose plants with better resistance to PHS.

Technical Abstract: Pre-harvest sprouting (PHS) in common wheat significantly reduces productivity and market value. A doubled-haploid (DH) population (386 lines) derived from a cross [SC8021-V2 (PHS tolerant) /AC Karma (moderately susceptible to PHS)] between two white-grained spring wheat genotypes, along with the parents was evaluated for sprouting score (SS) and falling number (FN) a laboratory measure of enzyme activity that indicates amount of PHS that occurred. The field trials were at two locations over two crop-seasons in India and genotyped by the Infinium iSelect 90K SNP array. Using composite interval mapping (CIM) and R/qtl, 29 main-effect QTL (MQTL) for SS and FN explaining 2.10-8.63 % (SS) and 2.10-10.93 % (FN) of the phenotypic variation were identified on 13 chromosomes. CIM exclusively revealed 9 MQTL (SS, 7; FN, 1; SS+FN, 1), R/qtl exclusively revealed 8 MQTL (SS, 6; FN, 2), and 12 MQTL (SS, 6; FN, 5; SS+FN, 1) were revealed by both; 16 MQTL were novel. Nineteen first-order epistatic interactions involving 18 SNPs were also detected. Validation of six stable and key MQTL for SS was conducted through the presence of their favorable alleles in the five extremely PHS tolerant DH lines. A set of 368 candidate genes encoding 42 distinct domains were identified; a majority (22) of these proteins were linked to ABA signaling. This study revealed a multifaceted role for candidate genes regulating PHS due to seed dormancy, hormone signaling, seed coat formation, starch metabolism, and stress adaptation. Three breeder-friendly KASP markers (two MQTL located on 2B and one MQTL on 4B) for sprouting score were also developed and validated for use in marker-assisted selection.