A whole‐genome, radiation hybrid mapping resource of hexaploid wheat

Abstract

SUMMARYGenerating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible. We developed a whole-genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high-density single nucleotide polymorphism (SNP) array. At the whole-genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR 1500 with a total map length of 6866 cR 1500 . The 7296 unique mapping bins provided a five-to eight-fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low-cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS-WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.

High‐resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTLQfhs.ifa‐5A

“…This repair pathway is error prone and can cause various kinds of genomic rearrangements such as interstitial deletions, insertions, inversions and translocations (Pipiras et al ., ; Puchta, ). Ionizing radiation‐induced chromosomal breaks occur randomly and are evenly distributed across the entire chromosomes, including pericentromeric regions (Kumar et al ., ; Tiwari et al ., ). Data matrix consists of presence and absence information of polymorphism‐independent specific sequences, allowing the utilization of any type of marker.…”

“…Moreover, RH mapping has successfully supported high‐resolution mapping of individual wheat chromosomes 1D (Kalavacharla et al ., ), 3B (Kumar et al ., ; Paux et al ., ), 6B (Kobayashi et al ., ) and 4A (Balcárková et al ., ), the D‐subgenome (Kumar et al . Riera‐Lizarazu et al ., ) and the whole genome of the hexaploid wheat (Tiwari et al ., ).…”

A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A

“…While we have developed RH map of chromosome 4A, Tiwari et al (2016) developed RH map for the whole wheat genome. Their map was constructed using iSelect 90K SNP array and fertile plants of RH lines derived from hybridization of tetraploid T. turgidum cv.…”

“…Chinese Spring. A total of 833 markers in three linkage groups (one for 4AS and two for 4AL) were identified for chromosome 4A ( Figure 4 ) and average mapping resolution was estimated to 2.4 Mb per mapping bin (Tiwari et al, 2016). Out of the 833 markers, 733 mapped in our RH map and 431 in consensus genetic map of 4A developed by Wang et al (2014).…”

“…Chromosome 4A RH and deletion maps are compared with the recombination consensus map of 4A chromosome (Wang et al, 2014) and whole genome RH map of bread wheat in which 4A is represented by linkage groups 4AS, 4AL1, and 4AL2 (Tiwari et al, 2016). Note the absence of SNP markers in centromeric region in the whole genome RH map and disagreement in marker order and the number between the whole genome RH map and the remaining maps.…”