The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping

Abstract

SummaryRecombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence‐based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome‐wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans‐acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans‐acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low‐recombining pericentromeric regions of chromosomes.

A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat

“…As expected, pairwise LD is consistently higher in peri‐centromeric regions (Figure b), even though markers are preferentially located in telomeric regions (Figure S7). These results are in agreement with the recombination frequency distribution observed in a bread wheat NAM (Jordan et al ., ). It is likely that the areas of high LD around centromeres are more extensive then what is apparent using the current marker set.…”

“…The EtNAM will side the multiparental populations available (Milner et al, 2016;Huang et al, 2012;Jordan et al, 2018;Mackay et al, 2014) and those in development in the Triticum species complex. It has been shown that the parallel employment of NAM families developed in closely related species can reinforce QTL findings (Mace et al, 2013), increasing their potential use in breeding efforts.…”

“…Conversely, nested association mapping (NAM) populations are produced by intercrossing one recurrent founder line with n other founder lines, which results in n recombinant inbred line (RIL) families that share the recurrent founder haplotype. The NAM design was developed in maize (McMullen et al, 2009) and later applied to several maize genetic backgrounds (Bauer et al, 2013) and different crops including soybean , sorghum (Bouchet et al, 2017), barley (Maurer et al, 2015;Nice et al, 2016), and bread wheat (Bajgain et al, 2016;Jordan et al, 2018).…”

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

“…We can now use this knowledge to break these negative correlations by purposely generating haplotypes that combine both beneficial traits. This will be facilitated by ongoing studies into the genetic basis of recombination in wheat, which could provide the knowledge to manipulate recombination rate distribution across chromosomes (Jordan et al ., ). With clearly defined haplotypes, we can also leverage the multiple layers of genomic information (e.g.…”

“…Much of this variation is studied through genetic populations composed of cultivars that differ for the trait(s) of interest. These include bi‐parental populations between two cultivars (Saintenac et al ., ), multi‐parent advanced generation inter‐cross (MAGIC) populations composed of between 4 and 16 cultivars (Huang et al ., ; Mackay et al ., ; Milner et al ., ; Dixon et al ., ), nested association mapping panels of multiple cultivars to a common parent (Jordan et al ., ), and association panels of 100 or more cultivars (Sukumaran et al ., ; Liu et al ., ). All of these types of populations are available in wheat and their relative merits are discussed elsewhere (Huang and Han, ).…”