Harnessing Landrace Diversity Empowers Wheat Breeding for Climate Resilience

Abstract

Breeding crops resilient to climate change is urgently needed to help ensure food security. A key challenge is to harness genetic diversity to optimise adaptation, yield, stress resilience and nutrition. We examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection of bread wheat (Triticum aestivum), a major global cereal, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just two of the seven ancestral groups of wheat, leaving five groups as previously untapped sources for breeding. This provides access to landrace-specific functional variations using structured germplasm, genotyping and informatics resources. Employing complementary genetic populations and approaches, we identified thousands of high-resolution quantitative trait loci (QTL) and significant marker–trait associations for major traits, revealing many Watkins-unique loci that can confer superior traits in modern wheat. Furthermore, we identified and functionally verified causative genes for climate-change adaptation, nutritional enhancement and resistance to wheat blast. Finally, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.

Unraveling wheat endosperm development: epigenetic regulation and novel regulators for enhanced yield and quality

“…S3F and G). A larger proportion of SNPs were significantly associated with starch and protein content in a previously characterized wheat population (Cheng et al, 2023), compared to other genomic regions (Fig. 3K and fig.…”

Development of a Next Generation SNP Genotyping Array for Wheat

“…Such focussed selection of samples coupled with the tendency to used sequence capture prior to sequencing could lead to the exclusion of rare alleles and a strong ascertainment bias (You et al ., 2018). Recent large scale skim sequencing (Cheng et al . 2023) of a highly diverse set of globally significant breeding and landrace accessions made available a new source of SNPs free of ascertainment bias and suitable for global users.…”

“…The SNP calls generated from skim sequence data from 315 wheat accessions (204 elite wheat lines and 111 wheat landraces taken from the Watkins "Core Collection" -Supplementary File S1) were used as the source of SNPs for haplotype optimisation (Cheng et al 2023). Varieties with >= 1% heterozygous loci were excluded.…”

“…The GWAS analysis was performed using the Watkins collection accessions and associated phenotype data as described in (Cheng et al, 2023) to compare the core 10M SNPs from the sequenced dataset (Cheng et al, 2023); SNPs from the Axiom™ Wheat Breeder's Genotyping Array (CerealsDB) and those of the TaNG Array v1.1. Extreme outlier values of phenotypic data were removed.…”

The wheat powdery mildew resistance gene Pm4 also confers resistance to wheat blast

“…Haplotype analysis was run across the genomic sequence of the AVR-Rmg8 resistance interval in the full Watkins collection (827 accessions) and a selection of modern wheat varieties (218 cultivars) using SY-Mattis as the reference genome 14,19 . A cluster heat map with 50 kb window size was generated to identify regions identical or near-identical to SY-Mattis which revealed that an additional 20 accessions of the Watkins collection carry sections of the 5.3 Mbp interval.…”