Genetic variation for domestication-related traits revealed in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) × ancestral rice, O. nivara, mapping population

G. C. Eizenga, P. L. Sanchez, A. K. Jackson, J. D. Edwards, Bonnie L Hurwitz, Rod A Wing, David A Kudrna

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3 Citations (Scopus)

Abstract

Oryza nivara is the ancestral species of cultivated rice (Oryza sativa). It has been the source of novel alleles for resistance to biotic and abiotic stresses, as well as yield improvement, lost during the course of domestication. 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 basal sheath and culm color, culm angle, days to heading, plant height, seed shattering, flag leaf length and width, panicle type and length, awn length and color, pericarp color, and seed color, 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 incorporate desirable, novel alleles for stress resistance and yield improvement, identified in rice wild species like O. nivara into elite, adapted O. sativa varieties.

Original languageEnglish (US)
Article number135
JournalMolecular Breeding
Volume37
Issue number11
DOIs
StatePublished - Nov 1 2017

Fingerprint

Oryza nivara
domestication
Oryza sativa
rice
genetic variation
Color
quantitative trait loci
color
Population
alleles
Alleles
Zizania aquatica
seed shattering
nucleotides
Seeds
Nucleotides
pericarp
biotic stress
heading
marker-assisted selection

Keywords

  • Domestication
  • Mapping population
  • Oryza nivara
  • Oryza sativa
  • Quantitative trait loci (QTL)
  • Simple sequence repeats (SSR)
  • Single nucleotide variation (SNV)
  • Yield components

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Agronomy and Crop Science
  • Genetics
  • Plant Science

Cite this

@article{631a69d51c93436bbd129082597583d2,
title = "Genetic variation for domestication-related traits revealed in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) × ancestral rice, O. nivara, mapping population",
abstract = "Oryza nivara is the ancestral species of cultivated rice (Oryza sativa). It has been the source of novel alleles for resistance to biotic and abiotic stresses, as well as yield improvement, lost during the course of domestication. 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 basal sheath and culm color, culm angle, days to heading, plant height, seed shattering, flag leaf length and width, panicle type and length, awn length and color, pericarp color, and seed color, 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 incorporate desirable, novel alleles for stress resistance and yield improvement, identified in rice wild species like O. nivara into elite, adapted O. sativa varieties.",
keywords = "Domestication, Mapping population, Oryza nivara, Oryza sativa, Quantitative trait loci (QTL), Simple sequence repeats (SSR), Single nucleotide variation (SNV), Yield components",
author = "Eizenga, {G. C.} and Sanchez, {P. L.} and Jackson, {A. K.} and Edwards, {J. D.} and Hurwitz, {Bonnie L} and Wing, {Rod A} and Kudrna, {David A}",
year = "2017",
month = "11",
day = "1",
doi = "10.1007/s11032-017-0734-5",
language = "English (US)",
volume = "37",
journal = "Molecular Breeding",
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T1 - Genetic variation for domestication-related traits revealed in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) × ancestral rice, O. nivara, mapping population

AU - Eizenga, G. C.

AU - Sanchez, P. L.

AU - Jackson, A. K.

AU - Edwards, J. D.

AU - Hurwitz, Bonnie L

AU - Wing, Rod A

AU - Kudrna, David A

PY - 2017/11/1

Y1 - 2017/11/1

N2 - Oryza nivara is the ancestral species of cultivated rice (Oryza sativa). It has been the source of novel alleles for resistance to biotic and abiotic stresses, as well as yield improvement, lost during the course of domestication. 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 basal sheath and culm color, culm angle, days to heading, plant height, seed shattering, flag leaf length and width, panicle type and length, awn length and color, pericarp color, and seed color, 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 incorporate desirable, novel alleles for stress resistance and yield improvement, identified in rice wild species like O. nivara into elite, adapted O. sativa varieties.

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KW - Domestication

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KW - Oryza nivara

KW - Oryza sativa

KW - Quantitative trait loci (QTL)

KW - Simple sequence repeats (SSR)

KW - Single nucleotide variation (SNV)

KW - Yield components

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