Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.
Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia.
Jorge
J
Duitama
Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia.
Alexander
A
Silva
Rice Research Station, Louisiana State University Agricultural Center, Rayne, Louisiana, United States of America.
Yamid
Y
Sanabria
Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia.
Daniel Felipe
DF
Cruz
Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia.
Constanza
C
Quintero
Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia.
Carolina
C
Ballen
Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia; Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement, Montpellier, France.
Mathias
M
Lorieux
Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Jamie Whitten Delta States Research Center, Stoneville, Mississippi, United States of America.
Brian
B
Scheffler
National Center for Genome Resources, Santa Fe, New Mexico, United States of America.
Andrew
A
Farmer
Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia.
Edgar
E
Torres
Rice Research Station, Louisiana State University Agricultural Center, Rayne, Louisiana, United States of America.
James
J
Oard
Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia.
Joe
J
Tohme
D000688:Amylose / Q000378:metabolism; D019295:Computational Biology; D056915:DNA Copy Number Variations; D005819:Genetic Markers / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D012275:Oryza / Q000235:genetics*; D000069600:Plant Breeding / Q000379:methods*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013214:Starch Synthase / Q000235:genetics / Q000378:metabolism
D005819:Genetic Markers; D010940:Plant Proteins; D000688:Amylose; C434607:granule-bound starch synthase I; D013214:Starch Synthase