TY - JOUR
T1 - Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date
AU - Canales, Francisco J.
AU - Montilla-Bascón, Gracia
AU - Bekele, Wubishet Abebe
AU - Howarth, Catherine
AU - Langdon, Tim
AU - Rispail, Nicolas
AU - Tinker, Nicholas A.
AU - Prats, Elena
N1 - This work was supported by the Spanish Ministry of Science and Innovation [AGL2016-78965AGR, PID2019-104518RB-100], (AEI/FEDER, UE) and regional government through the AGR-253 group, the European Regional and Social Development Funds, and Mobility Grant (FPI) 2018 from Ministry of Economy and Competitiveness of the Government of Spain [EEBB-I-18–12824]. FJC is holder of a FPI fellowship from the Spanish Ministry of Economy and Competitiveness [BES-2014–071044]. TL and CJH were supported by BBSRC grant BBS/E/W/0012843B.
PY - 2021/7/1
Y1 - 2021/7/1
N2 - Key message: Genomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement. Abstract: During the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.
AB - Key message: Genomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement. Abstract: During the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.
KW - Avena/genetics
KW - Genetic Association Studies
KW - Genetic Linkage
KW - Genetic Markers
KW - Genetics, Population
KW - Genotype
KW - Haplotypes
KW - Linkage Disequilibrium
KW - Mediterranean Region
KW - Polymorphism, Single Nucleotide
KW - Seeds/growth & development
UR - http://www.scopus.com/inward/record.url?scp=85103350884&partnerID=8YFLogxK
U2 - 10.1007/s00122-021-03805-2
DO - 10.1007/s00122-021-03805-2
M3 - Article
C2 - 33770189
SN - 0040-5752
VL - 134
SP - 2063
EP - 2077
JO - Theoretical and Applied Genetics
JF - Theoretical and Applied Genetics
IS - 7
ER -