ERA-CAPS: BARley yield associated Network

Agriculture faces the 'Grand Challenge' of feeding a growing population with less land, fewer resources, a changing climate, and increasing environmental quality demands from society. Thus, crops that produce more per unit area with fewer resources and are both resilient and adaptable will be key components in addressing this Grand Challenge. An important first step towards robust agricultural systems is to develop a deep understanding of the genetic control of yield. In barley, yield is determined by many components and the ability to increase yield through standard breeding approaches has slowed. The primary goal of this ERA-CAPS project is to identify genes that control yield-related traits in the small grain temperate cereal crop barley, and to begin to understand how they contribute to this complex phenotype. The three partners in this project will separately focus on seed, spike (inflorescence) and tiller (seed bearing stem) traits. The project will benefit from bringing together a collection of genetic resources and expertise from the three partners. Long-term community integration will be assured by sharing the resources, tools and information with the broader barley genetics and breeding community and by training the next generation of molecular breeders and scientists.

In barley, yield is determined by many components and the ability to increase yield through standard breeding approaches has slowed. Barley grain yield is impacted by three components including: seed (size and number), spike (inflorescence) and tillers (vegetative branches). The overall goal of this ERA-CAPS funded project is to identify genes that control morphological and developmental components of yield in barley, and to begin to understand how they contribute to this complex phenotype. The research leverages a previously exome captured sequenced germplasm panel, which will be phenotyped for yield-related traits. These data will provide the opportunity to gain an increased understanding of GxE interactions for key traits. The team will conduct transcriptome sequencing of six trait-related tissues per genotype and analyze how gene expression relates to trait development. To enable accurate quantification of transcript read depth, a reference transcript dataset will be developed by using deep paired-end Illumina RNA-seq and PacBio ISO-seq data from six tissues from cv. Morex. This will be used to quantify transcript abundance from RNA-seq data collected from the same six tissues sampled across the population. RNA-seq derived SNP alleles will supplement the exome capture SNPs and both SNP datasets and transcript read depth variation will be used for association analysis with yield-related traits. Gene co-expression networks will be constructed using reference transcript dataset from Morex and RNA-seq data from the six tissues sampled from the germplasm panel. Both datasets will be integrated to identify candidate genes or key regulators of yield related traits. Functional characterization of candidate genes will be initiated by identifying deleterious alleles from TILLING populations available in each of the three partner labs. The project will provide global community resources of broad impact including: a reference transcript dataset, additional SNPs derived from the landrace collection, and gene co-expression networks for exploring key regulatory genes and their relationship to yield-related traits.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.