Skip to main content
ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #336852

Research Project: Genomic Approaches and Genetic Resources for Improving Rice Yield and Grain Quality

Location: Dale Bumpers National Rice Research Center

Title: Genetic variation for traits associated with domestication identified in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) x ancestral rice, O. nivara, mapping population

Author
item Eizenga, Georgia
item Sanchez, Paul - University Of Arizona
item Jackson, Aaron
item Edwards, Jeremy
item Hurwitz, Bonnie - University Of Arizona
item Wing, Rod - University Of Arizona
item Kudrna, David - University Of Arizona

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 12/23/2016
Publication Date: 1/13/2017
Citation: Eizenga, G.C., Sanchez, P.L., Jackson, A.K., Edwards, J., Hurwitz, B.L., Wing, R.A., Kudrna, D. 2017. Genetic variation for traits associated with domestication identified in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) x ancestral rice, O. nivara, mapping population. Meeting Abstract. https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/24453.

Interpretive Summary:

Technical Abstract: Oryza nivara, the progenitor of cultivated rice, O. sativa, has been the source of novel alleles for resistance to biotic and abiotic stresses, as well as for yield improvement. Many of these alleles were lost during the domestication process. To determine the molecular changes that occurred during domestication, the O. sativa ssp. japonica variety, Nipponbare, from which a reference sequence (RefSeq) was developed, was crossed with the O. nivara accession (IRGC100897), from which BAC-end sequences (BES) were derived. The mapping population composed of 279 F2 progeny lines derived from this cross was phenotyped for 19 traits important to domestication and yield improvement, including vegetative and reproductive plant traits (culm and basal sheath color, culm angle, days to heading), mature plant traits (plant height, seed shattering, flag leaf length and width, panicle length and type) and seed traits (awn length and color, seed and pericarp color, seed length, width, length-to-width ratio, volume and surface area). The population was genotyped using 95 SSR markers and 114 single nucleotide variation (SNV) markers, selected by comparing the Nipponbare RefSeq and O. nivara BES. At least one major QTL was identified for each trait evaluated, and for 28 of the 46 QTL, the trait increase was attributed to the allele contributed by the O. nivara parent. Candidate genes were identified in 37 of the QTL regions. This study validated SNV markers that can be used for mapping in populations with a wild species parent. In the future, SNVs could be used for marker-assisted selection to introgress desirable, novel alleles for stress resistance and yield improvement, identified in rice wild species like O. nivara into elite, adapted O. sativa varieties.