A haplotype-led approach to increase the precision of wheat breeding

Abstract

Crop productivity must increase at unprecedented rates to meet the needs of the growing worldwide population. Exploiting natural variation for the genetic improvement of crops plays a central role in increasing productivity. Although current genomic technologies can be used for high-throughput identification of genetic variation, methods for efficiently exploiting this genetic potential in a targeted, systematic manner are lacking. Here, we developed a haplotype-based approach to identify genetic diversity for crop improvement using genome assemblies from 15 bread wheat (Triticum aestivum) cultivars. We used stringent criteria to identify identical-by-state haplotypes and distinguish these from near-identical sequences (~99.95% identity). We showed that each cultivar shares ~59 % of its genome with other sequenced cultivars and we detected the presence of extended haplotype blocks containing hundreds to thousands of genes across all wheat chromosomes. We found that genic sequence alone was insufficient to fully differentiate between haplotypes, as were commonly used array-based genotyping chips due to their gene centric design. We successfully used this approach for focused discovery of novel haplotypes from a landrace collection and documented their potential for trait improvement in modern bread wheat. This study provides a framework for defining and exploiting haplotypes to increase the efficiency and precision of wheat breeding towards optimising the agronomic performance of this crucial crop.

Multiple wheat genomes reveal global variation in modern breeding

“…Development of a wheat genome haplotype database. To identify haplotypes, pairwise chromosome alignments were performed between the RQA using MUMmer v.4.0, which were combined with pairwise nucleotide BLASTn analyses of the genes ± 2,000 bp using custom scripts in R v.3.6.1 (https://github.com/Uauy-Lab/ pangenome-haplotypes) 71 ( Supplementary Note 8). The resultant haplotypes were uploaded to an interactive viewer (http://www.…”

A duplicated copy of the meiotic geneZIP4preserves up to 50% pollen viability and grain number in polyploid wheat

“…6a, b). The recent availability of multiple sequenced wheat genomes has allowed the initial identification of haplotype blocks (Brinton et al, 2020), revealing different TaZIP4-B2 haplotypes. This information, combined with the availability of landrace diversity mapping populations (Wingen et al, 2017) and the pollen technique, can be used to rapidly identify any potential natural phenotype variation correlating with a specific TaZIP4-B2 haplotype, as well as to explore the stability of such phenotypes under variable temperatures.…”

Editorial: Proceedings of FSTP3 Congress–A Sustainable Durum Wheat Chain for Food Security and Healthy Lives

“…From a breeding standpoint, a pivotal issue remains having access to and leveraging beneficial allelic diversity to support genetic studies (Pozniak et al, 2012) and to enhance the performance of elite cultivars (Salvi and Tuberosa, 2015;Khalid et al, 2019;Brinton et al, 2020). A stepping stone to address this issue is the assembly of the Global Durum wheat Panel (GDP), a collection of 1,018 lines designed to identify beneficial alleles for durum wheat improvement (Mazzucotelli et al).…”