QTL mapping of pre-harvest sprouting resistance in a white wheat cultivar Danby

Abstract

One major and three minor QTLs for resistance to pre-harvest sprouting (PHS) were identified from a white wheat variety "Danby." The major QTL on chromosome 3A is TaPHS1, and the sequence variation in its promoter region was responsible for the PHS resistance. Additive × additive effects were detected between two minor QTLs on chromosomes 3B and 5A, which can greatly enhance the PHS resistance. Pre-harvest sprouting (PHS) causes significant losses in yield and quality in wheat. White wheat is usually more susceptible to PHS than red wheat. Therefore, the use of none grain color-related PHS resistance quantitative trait loci (QTLs) is essential for the improvement in PHS resistance in white wheat. To identify PHS resistance QTLs in the white wheat cultivar "Danby" and determine their effects, a doubled haploid population derived from a cross of Danby × "Tiger" was genotyped using genotyping-by-sequencing markers and phenotyped for PHS resistance in two greenhouse and one field experiments. One major QTL corresponding to a previously cloned gene, TaPHS1, was consistently detected on the chromosome arm 3AS in all three experiments and explained 21.6-41.0% of the phenotypic variations. A SNP (SNP-222) in the promoter of TaPHS1 co-segregated with PHS in this mapping population and was also significantly associated with PHS in an association panel. Gene sequence comparison and gene expression analysis further confirmed that SNP-222 is most likely the causal mutation in TaPHS1 for PHS resistance in Danby in this study. In addition, two stable minor QTLs on chromosome arms 3BS and 5AL were detected in two experiments with allele effects consistently contributed by Danby, while one minor QTL on 2AS was detected in two environments with contradicted allelic effects. The two stable minor QTLs showed significant additive × additive effects. The results demonstrated that pyramiding those three QTLs using breeder-friendly KASP markers developed in this study could greatly improve PHS resistance in white wheat.

Effects of TaPHS1 and TaMKK3-A Genes on Wheat Pre-Harvest Sprouting Resistance

“…However, in this study, the selected backcrossing progenies with both resistance genes still showed higher average germination rates than their PHS-resistant donors in most experiments (Tables 1 and 3), suggesting that other minor genes in both donor parents might also be important for reducing PHS [33]. Identifying and accumulating natural mutations and the non-grain color related resistance QTLs with TaPHS1 and TaMKK3-A could greatly enhance the PHS resistance in white wheat [3,19].…”

“…To avoid confusion between TaPHS1 and Phs1, we use TaPHS1 for the gene on 3AS and TaMKK3-A for the gene on 4AS hereafter. Although several other QTLs have been reported to be associated with PHS resistance [17][18][19], only TaPHS1 and TaMKK3-A have been cloned and validated to show major effects in multiple backgrounds [4][5][6]15].…”

Bulked segregant RNA-sequencing (BSR-seq) identified a novel rare allele of eIF4E effective against multiple isolates of BaYMV/BaMMV

“…The Amplifluor-like marker assay contained 40 ng template DNA (or 2 μl 1:10 diluted cDNA), 0.4 μM each of universal probes, 0.3 μM each of forward primers, 0.6 μM reverse primer, 0.2 mM dNTPs, 1 × Taq buffer (+Mg 2+ ) and 0.75 denaturation 5 s and 61 °C annealing 20 s in each cycle. The KASP marker was carried out following a standard KASP procedure (www.lgcgr oup.com) which was widely applied in bread wheat (Rasheed et al 2016;Shao et al 2018). The KASP reaction included 1 × KASP Master Mix, 0.4 mM MgCl 2 , 40 ng DNA template, 0.14 μM each of the allelespecific forward primers and 0.36 μM reverse primer in a final volume of 5 μl reaction.…”

Genetic Dissection of Seed Dormancy using Chromosome Segment Substitution Lines in Rice (Oryza sativa L.)

“…Seed dormancy is a highly complex trait and largely influenced by genetic and environmental factors [4]. Recent progress in plant genomics and various genetic populations has facilitated the identification of quantitative trait loci (QTLs) for seed dormancy in many species, for example, in Arabidopsis [5], Lepidium sativum [6], oilseed rape [7], sorghum [8], barley [9], and wheat [10][11][12].…”