Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.
BACKGROUND
The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers.


RESULTS
In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations.


CONCLUSIONS
Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.
Zhao
Keyan
K
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.
Wright
Mark
M
Kimball
Jennifer
J
Eizenga
Georgia
G
McClung
Anna
A
Kovach
Michael
M
Tyagi
Wricha
W
Ali
Md Liakat
ML
Tung
Chih-Wei
CW
Reynolds
Andy
A
Bustamante
Carlos D
CD
McCouch
Susan R
SR
D000483:Alleles; D000688:Amylose / Q000378:metabolism; D018556:Crops, Agricultural / Q000235:genetics*; D030541:Databases, Genetic; D017343:Genes, Plant / Q000235:genetics; D005808:Genes, Recessive / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D007113:Immunity, Innate / Q000235:genetics; D007178:Inbreeding; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D020161:Physical Chromosome Mapping; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011157:Population Dynamics; D012639:Seeds / Q000033:anatomy & histology / Q000235:genetics / Q000378:metabolism
D000688:Amylose