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G3 (Bethesda). 2017 Jun 7;7(6):1913-1926. doi: 10.1534/g3.117.041608.

Genetic Architecture of a Rice Nested Association Mapping Population.

Author information

1
Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511.
2
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511.
3
Department of Biostatistics, Yale University, New Haven, Connecticut 06511.
4
Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia.
5
Commissariat à L'énergie Atomique et aux Énergies Alternatives, Institut de Génomique, Genoscope, 91000 Evry, France.
6
Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia mathias.lorieux@ird.fr m.lorieux@cgiar.org.
7
Diversité, Adaptation, Développement des Plantes Research Unit, Institut de Recherche pour le Développement, F-34394 Montpellier, France.

Abstract

Describing the genetic diversity in the gene pool of crops will provide breeders with novel resources for varietal improvement. Nested Association Mapping (NAM) populations are uniquely suited for characterizing parental diversity through the shuffling and fixation of parental haplotypes. Here, we describe a set of 1879 rice NAM lines created through the selfing and single-seed descent of F1 hybrids derived from elite IR64 indica crossed with 10 diverse tropical japonica lines. Genotyping data indicated tropical japonica alleles were captured at every queried locus despite the presence of segregation distortion factors. Several distortion loci were mapped, both shared and unique, among the 10 populations. Using two-point and multi-point genetic map calculations, our datasets achieved the ∼1500 cM expected map size in rice. Finally, we highlighted the utility of the NAM lines for QTL mapping, including joint analysis across the 10 populations, by confirming known QTL locations for the trait days to heading.

KEYWORDS:

QTL mapping; computational biology; genetic maps; nested association mapping; plant genomics

PMID:
28450374
PMCID:
PMC5473768
DOI:
10.1534/g3.117.041608
[Indexed for MEDLINE]
Free PMC Article

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