Abstract
Multiparental cross designs for mapping quantitative trait loci (QTL) provide an efficient alternative to biparental populations because of their broader genetic basis and potentially higher mapping resolution. We describe the development and deployment of a recombinant inbred line (RIL) population in durum wheat (Triticum turgidum ssp. durum) obtained by crossing four elite cultivars. A linkage map spanning 2664cM and including 7594 single nucleotide polymorphisms (SNPs) was produced by genotyping 338 RILs. QTL analysis was carried out by both interval mapping on founder haplotype probabilities and SNP bi-allelic tests for heading date and maturity date, plant height and grain yield from four field experiments. Sixteen QTL were identified across environments and detection methods, including two yield QTL on chromosomes 2BL and 7AS, with the former mapped independently from the photoperiod response gene Ppd-B1, while the latter overlapped with the vernalization locus VRN-A3. Additionally, 21 QTL with environment-specific effects were found. Our results indicated a prevalence of environment-specific QTL with relatively small effect on the control of grain yield. For all traits, functionally different QTL alleles in terms of direction and size of genetic effect were distributed among parents. We showed that QTL results based on founder haplotypes closely matched functional alleles at known heading date loci. Despite the four founders, only 2.1 different functional haplotypes were estimated per QTL, on average. This durum wheat population provides a mapping resource for detailed genetic dissection of agronomic traits in an elite background typical of breeding programmes.
Highlights
Quantitative trait locus (QTL) analysis on multiparental populations occupies an intermediate niche between conventional linkage mapping based on biparental populations and association mapping in germplasm collections
NCCR captured 76% of the single nucleotide polymorphisms (SNPs) alleles from the reference collection, with a SNP rate of 10.3% (19.7% in the reference collection). These results indicate that the genetic diversity represented by the NCCR founders represents well the overall range of diversity in durum wheat elite germplasm
The NCCR linkage map included 7594 SNPs and spanned 2664 cM (1188 cM for the A genome and 1476 cM for the B genome, details reported in Table 1 and File S1), distributed in 14 linkage groups
Summary
Quantitative trait locus (QTL) analysis on multiparental populations occupies an intermediate niche between conventional linkage mapping based on biparental populations and association mapping in germplasm collections. The idea of combining the genomes of multiple founders to ensure segregation for multiple QTL was first developed in mouse genetics with the name of heterogeneous stocks (Demarest et al, 2001; McClearn et al, 1970), which could be considered as an extension of the biparental advanced intercross lines (AILs) approach (Darvasi and Soller, 1995) to include broader genetic diversity. Linkage mapping in biparental populations often detects QTL with large support intervals because of limited recombination (Doerge, 2002; Holland, 2007). Mapping of QTL in multiparental populations is expected to combine the advantages of the two approaches: high number of informative crossovers, possibility to interrogate multiple alleles, limited population structure effects (Rebai and Goffinet, 2000). Only a few balanced multiparental populations have been developed in Arabidopsis thaliana (Huang et al, 2011; Kover et al, 2009), tomato (Pascual et al, 2014), bread wheat (Huang et al, 2012; Mackay et al, 2014; Rebetzke et al, 2014; Thepot et al, 2015) and rice (Bandillo et al, 2013)
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