A multiparental cross population for mapping QTL for agronomic traits in durum wheat (Triticum turgidum ssp. durum)

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 2664 cM 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.

Keywords: QTL; SNP; Triticum turgidum; agronomic traits; founder haplotypes; multiparental cross.

Figure 1

Marker density along chr. 6A and chr. 7A. From top to bottom: bread wheat consensus map (blue‐dotted plot. From Wang et al., 2014), durum wheat consensus map (green‐dotted plot. From Maccaferri et al., 2014) and NCCR map (black‐dotted plot; this study). X‐axis: genetic map of the chromosome (cM); red triangles: position of anchor markers; y‐axis: SNP density (1 cM‐bin), sliding window of 7 cM. Centromere positions are shown as grey rectangles below the x‐axis.

Figure 2

Proportion of 338 RILs assigned to each of the four founders across the NCCR linkage map.

Figure 3

RIL frequency distributions for the four traits investigated in this study. Mean values of the founder lines are identified by coloured bars: Neodur (green), Claudio (red), Colosseo (orange) and Rascon/2*Tarro (blue). For each trait, the population mean value is indicated by an arrow.

Figure 4

NCCR linkage map reporting QTL positions for heading date (HD), maturity date (MD), plant height (PH) and grain yield (GY, data combined across environments. Green bars: QTL mapped by IBD‐CIM. Red bars: QTL mapped by IBS‐SMA (also denoted by ‘_t’ suffix). For each QTL, bar and bar tick represent the LOD drop confidence interval and the LOD peak position, respectively.

Figure 5

Functional effects, SNP‐based haplotypes and allelic causal variation at QHd.ubo‐2A (a), QHd.ubo‐2B (b) and QHd.ubo‐7A.2 (c). For each QTL, the functional (phenotypic) QTL effects as estimated by IBD‐CIM and IBS‐SMA are reported on the top left and top right, respectively (QTL effects were always estimated taking Rascon/2*Tarro (RT), as reference haplotype); SNP‐based haplotypes in the QTL confidence interval are reported on the bottom left; parental alleles at the most significant SNP marker from the IBS‐SMA are reported on central right; allelic variation observed at the causal gene is reported as number codes on the right‐bottom corner of each subsection (different alleles are represented by different numbers).