A global barley panel revealing genomic signatures of breeding in modern cultivars

Abstract

18The future of plant cultivar improvement lies in the evaluation of genetic resources from 19 currently available germplasm. Recent efforts in plant breeding have been aimed at 20 developing new and improved varieties from poorly adapted crops to suit local environments. 21 However, the impact of these breeding efforts is poorly understood. Here, we assess the 22 contributions of both historical and recent breeding efforts to local adaptation and crop 23 improvement in a global barley panel by analysing the distribution of genetic variants with 24 respect to geographic region or historical breeding category. By tracing the impact breeding 25 had on the genetic diversity of barley released in Australia, where the history of barley 26 production is relatively young, we identify 69 candidate regions within 922 genes that were 27 under selection pressure. We also show that modern Australian barley varieties exhibit 12% 28 higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for 29 agriculturally relevant traits across a diverse range of Australian environments suggests that 30 genomic regions under strong breeding selection and their candidate genes are closely 31 associated with key agronomic traits. In conclusion, our combined dataset and germplasm 32 collection provide a rich source of genetic diversity that can be applied to understanding and 33 improving environmental adaptation and enhanced yields. 35Author summary 36 Today's gene pool of crop genetic diversity has been shaped during domestication and more 37 recently by breeding. Genetic diversity is vital for crop species to be able to adapt to 38 changing environments. There is concern that recent breeding efforts have eroded the genetic 39 diversity of many domesticated crops including barley. The present study assembled a global 40 panel of barley genotypes with a focus on historical and modern Australian varieties.41 Genome-wide data was used to detect genes that are thought to have been under selection 3 42 during crop breeding in Australian barley. The results demonstrate that despite being more 43 extensively bred, modern Australian barley varieties exhibit higher genetic diversity than 44 historical cultivars, countering the common perception that intensive breeding leads to 45 genetic erosion of adaptive diversity in modern cultivars. In addition, some loci (particularly 46 those related to phenology) were subject to selection during the introduction of other barley 47 varieties to Australia -these genes might continue to be important targets in breeding efforts 48 in the face of changing climatic conditions. 49 50 51The diversity of the existing genetic pool for commercially important plant species has been 52 shaped during plant domestication, human migration, varietal selection processes and, more 53 recently, breeding. However, there is concern that breeding efforts have eroded genetic 54 variation, thereby resulting in a narrow range of genotypes in the current gene pools of 55 domesticated crops [1...

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Genome-wide association mapping reveals novel genes associated with coleoptile length in a worldwide collection of barley

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