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

Abstract

Summary The Ethiopian plateau hosts thousands of durum wheat ( Triticum turgidum subsp. durum ) farmer varieties ( FV ) with high adaptability and breeding potential. To harness their unique allelic diversity, we produced a large nested association mapping ( NAM ) population intercrossing fifty Ethiopian FV s with an international elite durum wheat variety (Asassa). The Ethiopian NAM population (Et NAM ) is composed of fifty interconnected bi‐parental families, totalling 6280 recombinant inbred lines ( RIL s) that represent both a powerful quantitative trait loci ( QTL ) mapping tool, and a large pre‐breeding panel. Here, we discuss the molecular and phenotypic diversity of the Et NAM founder lines, then we use an array featuring 13 000 single nucleotide polymorphisms ( SNP s) to characterize a subset of 1200 Et NAM RIL s from 12 families. Finally, we test the usefulness of the population by mapping phenology traits and plant height using a genome wide association ( GWA ) approach. Et NAM RIL s showed high allelic variation and a genetic makeup combining genetic diversity from Ethiopian FV s with the international durum wheat allele pool. Et NAM SNP data were projected on the fully sequenced AB genome of wild emmer wheat, and were used to estimate pairwise linkage disequilibrium ( LD ) measures that reported an LD decay distance of 7.4 Mb on average, and balanced founder contributions across Et NAM families. GWA analyses identified 11 genomic loci individually affecting up to 3 days in flowering time and more than 1.6 cm in height. We argue that the Et NAM is a powerful tool to support the production of new durum wheat varieties targeting local and global agriculture.

Genetic architecture of polyphenol oxidase activity in wheat flour by genome‐wide association study

“…This was consistent with Kidane et al. (2019), where LD decay was 7.4 Mb on average, ranging from 3.7 (chromosome 4A) to 18.7 Mb (chromosome 3B).…”

The Wheat 660K SNP array demonstrates great potential for marker‐assisted selection in polyploid wheat

“…Therefore, SNP arrays have been widely used by many breeders in a variety of academic research, including genome‐wide association (Guo et al , 2017; Kidane et al , 2019), linkage map construction and QTL mapping (Cui et al , 2017; Jin et al , 2016), population structure, and phylogenetic analysis (Kidane et al , 2019; Valluru et al , 2017). In the present study, we selected seven widely used high‐throughput wheat arrays (Wheat 9K, 15K, 35K, 55K, 90K, 820K and 660K arrays) and compared their performance in terms of SNP number, distribution, density and associated genes to assess their value and provide guidance for their better application in marker‐assisted breeding at the wheat genome level.…”

Integrating Conventional and Participatory Crop Improvement for Smallholder Agriculture Using the Seeds for Needs Approach: A Review

“…A preliminary characterization of 1,200 RILs from 12 families had shown that the more diverse and high yielding families are those bridging Ethiopian gene-pool with the international allele pool. The Ethiopian NAM, named EtNAM, has shown that it is possible to achieve significant steps in germplasm improvement by using alleles found in farmer varieties (Kidane et al, 2019).…”