Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties

Sales Clemente, Ester (Universidad de Zaragoza) ; Viruel Sánchez, Juan ; Domingo Carrasco, Concha ; Marqués Falcó, Luis

Resumen: A pool of 200 traditional, landraces and modern elite and old cultivars of rice, mainly japonica varieties adapted to temperate regions, have been used to perform a genome wide association study to detect chromosome regions associated to low temperature germination (LTG) regulation using a panel of 1672 SNP markers. Phenotyping was performed by determining growth rates when seeds were germinated at 25Ê and 15ÊC in order to separate the germination vigorousness from cold tolerance effects. As expected, the ability to produce viable seedlings varied widely among rice cultivars and also depended greatly on temperature. Furthermore, we observed a differential response during seed germination and in coleoptile elongation. Faster development at 15ÊC was observed in seeds from varieties traditionally used as cold tolerant parents by breeders, along with other potentially useful cultivars, mainly of Italian origin. When phenotypic data were combined with the panel of SNPs for japonica rice cultivars, significant associations were detected for 31 markers: 7 were related to growth rate at 25ÊC and 24 to growth rates at 15Ê. Among the latter, some chromosome regions were associated to LTG while others were related to coleoptile elongation. Individual effects of the associated markers were low, but by combining favourable alleles in a linear regression model we estimated that 27 loci significantly explained the observed phenotypic variation. From these, a core panel of 13 markers was selected and, furthermore, two wide regions of chromosomes 3 and 6 were consistently associated to rice LTG. Varieties with higher numbers of favourable alleles for the panels of associated markers significantly correlated with increased phenotypic values at both temperatures, thus corroborating the utility of the tagged markers for marker assisted selection (MAS) when breeding japonica rice for LTG.

Idioma: Inglés

DOI: 10.1371/journal.pone.0183416

Año: 2017

Publicado en: PLoS ONE 12, e0183416 (2017), [18 pp.]
ISSN: 1932-6203

Factor impacto JCR: 2.766 (2017)

Categ. JCR: MULTIDISCIPLINARY SCIENCES rank: 14 / 63 = 0.222 (2017) - Q1 - T1

Factor impacto SCIMAGO: 1.164 - Agricultural and Biological Sciences (miscellaneous) (Q1) - Medicine (miscellaneous) (Q1) - Biochemistry, Genetics and Molecular Biology (miscellaneous) (Q1)

Financiación: info:eu-repo/grantAgreement/ES/MINECO/IPT-2011-1244-010000

Tipo y forma: Article (Published version)

Área (Departamento): Área Producción Vegetal (Dpto. CC.Agrar.y Medio Natural)