Global Role of Crop Genomics in the Face of Climate Change

Abstract

The development of climate change resilient crops is necessary if we are to meet the challenge of feeding the growing world's population. We must be able to increase food production despite the projected decrease in arable land and unpredictable environmental conditions. This review summarizes the technological and conceptual advances that have the potential to transform plant breeding, help overcome the challenges of climate change, and initiate the next plant breeding revolution. Recent developments in genomics in combination with high-throughput and precision phenotyping facilitate the identification of genes controlling critical agronomic traits. The discovery of these genes can now be paired with genome editing techniques to rapidly develop climate change resilient crops, including plants with better biotic and abiotic stress tolerance and enhanced nutritional value. Utilizing the genetic potential of crop wild relatives (CWRs) enables the domestication of new species and the generation of synthetic polyploids. The high-quality crop plant genome assemblies and annotations provide new, exciting research targets, including long non-coding RNAs (lncRNAs) and cis-regulatory regions. Metagenomic studies give insights into plant-microbiome interactions and guide selection of optimal soils for plant cultivation. Together, all these advances will allow breeders to produce improved, resilient crops in relatively short timeframes meeting the demands of the growing population and changing climate.

The barley leaf rust resistance gene Rph3 encodes a putative executor protein

“…Major bottlenecks in genetic variation in many crops were caused by domestication and many variations remained in the wild gene pool 100, 101 . Wild barley that freely crosses with cultivated barley is a well-known source of allelic variation 102,103 . The Rph3 gene is a functional allele that confers resistance, and its semidominant behaviour can be accounted for as a gene dosage effect.…”

“…Based on the protein similarity of RPH3 and NCED, the involvement in ABA biosynthesis in Rph3-induced resistance to P. hordei can be hypothesized. Major bottlenecks in genetic variation in many crops were caused by domestication and many variations remained in the wild gene pool 100, 101 . Wild barley that freely crosses with cultivated barley is a well-known source of allelic variation 102,103 .…”

Fused Graphical Lasso Recovers Flowering Time Mutation Genes in Arabidopsis thaliana

“…In the last few centuries, plant breeders successfully used crossing and selection to improve the agronomic character of cultivated crops, such as wheat, maize, rice, barley and others, resulting in dramatic increases in food production [7]. However, this selective breeding among relatively few high yield varieties has resulted in a significant reduction in genetic diversity and trait diversity in major crops [7,8], contributing to the loss of certain genes that are responsible for efficiency or adaptation to stress(es) [8,9]. During the course of evolution, nature has evolved new genes and shuffled and selected these genes in a wide range of environments to produce the diversity evidenced in wild species [8].…”

“…In order to enhance the rate of genetic gain [10] and to develop climate resilient varieties, it is important to identify these genes in crop wild relatives (CWR) and carry out their controlled incorporation into novel germplasm [8]. With the recent technological innovations including the development of rapid and cheap sequencing technologies, genomics-assisted breeding is considered to have the greatest potential for overcoming these challenges [2,7]. The discovery of these genes can now be paired with genome editing techniques such as CRISPR/Cas9 to rapidly develop climate change resilient crops, including plants with better biotic and abiotic stress tolerance and enhanced nutritional value [7].…”

“…With the recent technological innovations including the development of rapid and cheap sequencing technologies, genomics-assisted breeding is considered to have the greatest potential for overcoming these challenges [2,7]. The discovery of these genes can now be paired with genome editing techniques such as CRISPR/Cas9 to rapidly develop climate change resilient crops, including plants with better biotic and abiotic stress tolerance and enhanced nutritional value [7]. For developing varieties with high yield under changing climate conditions, the following traits have been suggested by biologists for further investigation [11]: (a) increased root/shoot ratio, (b) vernalization periods, (c) maturity, (d) regulation of node formation/internode distance, (e) harvest index variations and (f) allelopathy.…”