A new genetic and deletion map of wheat chromosome 5A to detect candidate genes for quantitative traits

Abstract

In the present study, a detailed deletion\ud map for wheat chromosomes 5A and 5B is reported, as\ud well as an integrated genetic linkage map of chromosome\ud 5A enriched with single nucleotide polymorphism\ud (SNP) markers, useful both for comparison\ud studies with other existing maps and for mapping\ud major genes and quantitative trait loci (QTLs). Physical\ud mapping of 5,011 SNP markers was obtained\ud using Chinese Spring bin deletion lines for the\ud homoeologous chromosomes of group 5; \ud 509 SNPs were also genetically mapped in a recombinant inbred\ud line population segregating for chromosome 5A only,\ud obtained by crossing the cultivar Chinese Spring and\ud the disomic substitution line Chinese Spring-5A\ud dicoccoides. The whole 5A genetic map, containing\ud 572 markers, covered a total length of 248.7 cM\ud distributed among three linkage groups of 83.5, 117.8\ud and 47.4, respectively. The majority of SNP markers\ud physically mapped on 5A were mapped to a unique\ud bin, while a small percentage was assigned a double\ud location, suggesting the presence of a segment of 5A\ud short arm which may have undergone a duplication\ud followed by an insertion into the long arm of the same\ud chromosome. A QTL analysis for yield components\ud was performed, identifying a major QTL in the subtelomeric\ud region of chromosome 5A, corresponding to\ud the 5AL15-0.67-0.78 bin; the chromosome segment\ud was 23.5 cM long and included 111 markers. Candidate\ud genes for yield components on chromosome 5A\ud were identified through a syntenic genomic approach\ud by comparison with genomes of model species.\ud Putative function analysis revealed genes involved in\ud basic metabolism and in stress condition responses,\ud including heat shock proteins, chaperones, serine/\ud threonine protein kinases and membrane transporters,\ud located in the region of the QTL. This information\ud represents an important step for map-based and\ud candidate gene-based cloning of yield QTLs

Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach

“…To increase the integration of genetic and physical data, a neighbor map for each chromosome arm was developed following procedures already adopted for wheat and other cereals (Mayer et al, 2011; Paux et al, 2008; Philippe et al, 2012). A high‐density genetic map of CS × CS5A_90K recently released (Gadaleta et al, 2014) based on EST‐derived 90K_SNPs (Infinium iSelect 90K BeadChip array) and SSRs was employed as a framework on which markers from additional genetic maps were individually integrated. In the CS × CS5A map population, 5A loci segregate in a CS background, therefore this population is likely to be the best for anchoring and ordering MTP contigs made of CS BAC clones.…”

“…This latter interval corresponds to the maximum distance within which, even choosing different backbone markers, the order of inferred markers does not change. The CS × CS5A 90K map (Gadaleta et al, 2014) was integrated with the CS × CS5A map developed in this work with SSRs, ESTs, COSs, and TE‐based markers to define a robust scaffold of common markers. Because of the lack of a sufficiently conserved subset of common markers, only one marker was integrated from the DV × G3 map into the neighbor map.…”

“…A neighbor mapping approach was undertaken to achieve a densely covered map for an efficient anchoring of the physical map according to the method introduced by Cone et al (2002). The neighbor maps, one for each chromosome arm, were produced integrating the CS × CS5A framework map (Gadaleta et al, 2014) with maps from the following sources: (i) an SSR‐based consensus map developed from four maps (‘Synthetic’ × ‘Opata’, ‘RL4452’ × ‘AC Domain’, ‘Wuhan #1’ × ‘Maringa’, and ‘Superb’ × ‘BW278’; Somers et al, 2004); (ii) six maps developed from biparental populations: ‘Nanda2419’ × ‘Wangshuibai’ (Xue et al, 2008), CS × Re, DV × G3 (both developed in this work), and a Lt × MG map made using the Illumina Infinium 90K SNP array (Desiderio et al, 2014), and (iii) the 90K_SNP‐based consensus map obtained from eight doubled‐haploid populations published by Wang et al (2014).…”

Quality characteristics of parental lines of wheat mapping populations

“…The glutenin composition, in particular, has been used to establish a quality score, as extensively reviewed by Shewry et al (1992). The allelic variations of high molecular weight glutenin suba Gadaleta et al 2012Gadaleta et al , 2014 b Piarulli et al 2012;c Blanco et al 1998c Blanco et al , 2001c Blanco et al , 2002 units (HMW-GS) and of ω-and γ-gliadins in the wheat cultivars and accessions considered are reported in Table 3. Three different HMW-GS alleles at the Glu-A1 locus, 5 HMW-GS alleles at the Glu-B1 locus, and 5 different gliadin alleles at the Gli-B1 locus, were observed.…”

Varietal traceability of bread ‘Pane Nero di Castelvetrano’ by denaturing high pressure liquid chromatography analysis of single nucleotide polymorphisms

“…DNA genotyping by SNPs has successfully been applied to the construction of high density genetic maps in wheat (Cavanagh et al, 2013;Colasuonno et al, 2014;Gadaleta et al, 2014;Maccaferri et al, 2014;Wang et al, 2014) and to varietal traceability in the food-chain with examples reported for olive oil (Consolandi et al, 2008) but, up to now, not in case of wheatbased foods.…”