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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Improvement Research » Research » Publications at this Location » Publication #418755
Research Project: Improvement of Disease and Pest Resistance in Barley, Durum, Oat, and Wheat Using Genetics and Genomics

Location: Cereal Crops Improvement Research

Title: Cytonuclear analysis of barley spike traits using a cytoplasm-aware population

Author
item BODENHEIMER, SCHEWACH - Volcani Center (ARO)
item BDOLACH, EYAL - Volcani Center (ARO)
item BEERY, AVITAL - Volcani Center (ARO)
item Yang, Shengming
item KOEING, DANIEL - University Of California, Riverside
item FRIMAN, EYAL - Volcani Center (ARO)

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 12/5/2023
Publication Date: 1/7/2024
Citation: Bodenheimer, S., Bdolach, E., Beery, A., Yang, S., Koeing, D., Friman, E. 2024. Cytonuclear analysis of barley spike traits using a cytoplasm-aware population. Meeting Abstract. Poster No. PO43.

Interpretive Summary:

Technical Abstract: Crop wild relatives are a sought-after resource for the improvement of existing crop varieties and for identifying loci underlying domestication. The population designs used can be broadly divided into diversity panels, bi- and multiparental populations, and diallel crosses, which all focus mainly on nuclear diversity. Here, we present the barley cytonuclear multi parent population (CMPP), which consists of 924 doubled haploid lines divided into 10 subfamilies, each showcasing segregation of both nuclear and cytoplasmic wild alleles. Analysis of key spike traits collected in four field trials during 2022-2024 showed that the cytoplasmic origin affects all tested best linear unbiased predictions (BLUPs), and that specific wild cytoplasms also change trait stability indices for thousand grain weight (TGW). Nuclear SNP data was scored using the iSelect 50K platform and allowed us to exclude that trait differences between cytoplasmic groups are explained by nuclear drift. Using the marker data, the CMPP’s design also allowed us to efficiently scan for cytonuclear epistasis, resulting in 13 cytonuclear QTL (cnQTL), where the nuclear allele effect is conditioned by the cytoplasmic background. Juxtaposing the identified cnQTL with marker-trait associations (MTAs) from classical GWAS analyses showed that these loci are mostly missed with nuclear-only models, thereby highlighting the importance of cytoplasm-aware population designs. We also incorporated cytonuclear interaction information into genomic prediction models, yielding a relative increase in cross-validation accuracy of up to 21.7 percent for Fruiting efficiency at maturity (FEm). Looking forward, cnQTL can present a starting point for the molecular dissection of cytonuclear interactions, while cytonuclear epistasis-based genomic prediction models using populations such as the CMPP can potentially improve breeding outcomes.