Exome sequences and multi‐environment field trials elucidate the genetic basis of adaptation in barley

Autor: Enes Yakışır, Ian K. Dawson, Noemi Trabanco, Chiara Ferrandi, Robbie Waugh, Laura Rossini, Mária Megyeri, Joanne Russell, Hakan Özkan, Martin Mascher, Peter Werner, Daniela Bustos-Korts, Stefano Delbono, Péter Mikó, Fred A. van Eeuwijk, Davide Cammarano, Esra Çakır, Márta Molnár-Láng, Nils Stein, Luigi Cattivelli, Allan Booth, Davide Guerra, Stylianos Kyriakidis, Benjamin Kilian, Ezequiel L. Nicolazzi, Alessandro Tondelli, Francesco Strozzi
Přispěvatelé: Çukurova Üniversitesi
Rok vydání: 2019
Předmět:
0106 biological sciences
0301 basic medicine
Acclimatization
adaptation
Plant Science
Wiskundige en Statistische Methoden - Biometris
01 natural sciences
Linkage Disequilibrium
H. vulgare ssp. vulgare
Exome
genotype-by-environment interactions
2. Zero hunger
Geography
food and beverages
genetic diversity
PE&RC
Biometris
Phenotype
Trait
Original Article
Crops
Agricultural
Genotype
Quantitative Trait Loci
Context (language use)
Biology
Polymorphism
Single Nucleotide
Life history theory
genotype‐by‐environment interactions
03 medical and health sciences
Circadian Clocks
Exome Sequencing
Genetics
Domestication
Mathematical and Statistical Methods - Biometris
Genetic diversity
business.industry
Genetic Variation
barley
Hordeum
Original Articles
Cell Biology
15. Life on land
Plant Breeding
030104 developmental biology
Haplotypes
Evolutionary biology
Agriculture
common garden trials
exome sequence haplotypes
Adaptation
business
Genome-Wide Association Study
010606 plant biology & botany
Zdroj: Plant Journal 99 (2019) 6
The Plant Journal
Plant Journal, 99(6), 1172-1191
ISSN: 1365-313X
0960-7412
DOI: 10.1111/tpj.14414
Popis: Summary Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi‐environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype‐by‐environment (G×E) modelling. Sub‐populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock‐related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large‐effect alleles. Our analysis supports a gene‐level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.
Significance Statement We analysed exome sequence data and life history traits measured in multi‐environment trials of a diverse panel of 371 domesticated barley lines to explore the genetics of crop adaptation. G×E interactions indicated adaptation profiles that varied for sub‐populations defined from exomic data. Exploration of circadian clock‐related genes associated with days to heading revealed complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large effect alleles. Analysis provides practical information for future crop breeding.
Databáze: OpenAIRE
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