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Genetic diversity and population structure in a rice drought stress panel

Published online by Cambridge University Press:  12 September 2014

Dindo A. Tabanao ,
Arnel E. Pocsedio ,
Jonalyn C. Yabes ,
Marjohn C. Niño ,
Reneth A. Millas ,
Neah Rosandra L. Sevilla ,
Xiao Yulong  and
Jianming Yu
Dindo A. Tabanao*
Affiliation:
Plant Breeding and Biotechnology Division, Philippine Rice Research Institute, Maligaya, Science City of Muñoz 3119, Nueva Ecija, Philippines
Arnel E. Pocsedio
Affiliation:
Plant Breeding and Biotechnology Division, Philippine Rice Research Institute, Maligaya, Science City of Muñoz 3119, Nueva Ecija, Philippines
Jonalyn C. Yabes
Affiliation:
Plant Breeding and Biotechnology Division, Philippine Rice Research Institute, Maligaya, Science City of Muñoz 3119, Nueva Ecija, Philippines
Marjohn C. Niño
Affiliation:
Plant Breeding and Biotechnology Division, Philippine Rice Research Institute, Maligaya, Science City of Muñoz 3119, Nueva Ecija, Philippines
Reneth A. Millas
Affiliation:
Plant Breeding and Biotechnology Division, Philippine Rice Research Institute, Maligaya, Science City of Muñoz 3119, Nueva Ecija, Philippines
Neah Rosandra L. Sevilla
Affiliation:
Plant Breeding and Biotechnology Division, Philippine Rice Research Institute, Maligaya, Science City of Muñoz 3119, Nueva Ecija, Philippines
Xiao Yulong
Affiliation:
Jiangxi Academy of Agricultural Science, No. 602 Nanlian Road, Nanchang, Jiangxi, P. R. China
Jianming Yu
Affiliation:
Department of Agronomy, Iowa State University, Ames, IA50011, USA
*
*Corresponding author. E-mail: da.tabanao@philrice.gov.ph
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Abstract

A drought stress panel composed of diverse accessions selected from upland, aerobic, rainfed lowland and irrigated lowland environments, was assembled to serve as germplasm for aerobic adaptation breeding. Aerobic rice requires significant levels of tolerance to drought stress due to intermittent water deficit and high soil impedance caused by aerobic conditions. Genomic information may be utilized to investigate the nature of the panel to guide varietal improvement. Using 153 simple sequence repeat and 384 single nucleotide polymorphism markers, the aim of the study was to compare the allelic properties of the two marker types, infer population structure of the panel, and estimate kinship among the accessions. There was a general agreement between the results derived from the two marker types. Marker alleles were found to occur at low frequencies, as the panel was composed mostly of improved accessions with some landraces. The panel clustered into japonica (JA), aus (AU), upland-adapted indica (UL) and lowland-adapted indica (LL) subpopulations. The AU and JA subpopulations were more divergent from the rest of the subpopulations than were the LL and UL subpopulations. Average marker-based kinship for related accessions was less than 0.20, indicating a low degree of genetic relatedness in the panel. Within the LL and UL subpopulations, the low levels of kinship imply that there is still much genetic gain to be expected from utilizing the accessions in breeding. Thus, an understanding of the genetic variation in the panel suggests focusing on improving the mean in the short term, and tapping into the exotic alleles from the AU and JA subpopulations when genetic gain declines.

Keywords

genetic diversitypopulation structuresimple sequence repeatssingle nucleotide polymorphismsrice
Type
Research Article
Information
Plant Genetic Resources , Volume 13 , Issue 3 , November 2015 , pp. 195 - 205
Copyright
Copyright © NIAB 2014 

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