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Chai C, Shankar R, Jain M, Subudhi PK. Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice. Sci Rep 2018; 8:14218. [PMID: 30242197 PMCID: PMC6155081 DOI: 10.1038/s41598-018-32513-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 09/10/2018] [Indexed: 12/13/2022] Open
Abstract
Analyzing the genome level DNA polymorphisms between weedy and cultivated rice is crucial to elucidate the molecular basis of weedy and agronomic traits, which in turn can enhance our ability to control weedy rice and its utilization for rice improvement. Here, we presented the genome-wide genetic variations between a weedy rice accession PSRR-1 and two cultivated rice accessions, Bengal and Nona Bokra, belonging to japonica and indica subspecies, respectively. The total number of SNPs and InDels in PSRR/Bengal was similar to that of Nona Bokra/Bengal, but was three times greater than that of PSRR/Nona Bokra. There were 11546 large-effect SNPs/InDels affecting 5673 genes, which most likely differentiated weedy rice from cultivated rice. These large effect DNA polymorphisms were mostly resulted in stop codon gain and least by start codon loss. Analysis of the molecular functions and biological processes of weedy rice specific SNPs/InDels indicated that most of these genes were involved in protein modification/phosphorylation, protein kinase activity, and protein/nucleotide binding. By integrating previous QTL mapping results with the DNA polymorphisms data, the candidate genes for seed dormancy and seed shattering were narrowed down. The genomic resource generated in this study will facilitate discovery of functional variants for weedy and agronomic traits.
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Affiliation(s)
- Chenglin Chai
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Rama Shankar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Prasanta K Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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Plekhanova E, Vishnyakova MA, Bulyntsev S, Chang PL, Carrasquilla-Garcia N, Negash K, Wettberg EV, Noujdina N, Cook DR, Samsonova MG, Nuzhdin SV. Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits. Sci Rep 2017; 7:4816. [PMID: 28684880 PMCID: PMC5500531 DOI: 10.1038/s41598-017-05087-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 05/24/2017] [Indexed: 12/30/2022] Open
Abstract
The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic 'agro islands', and in genotype-to-phenotype relationships resembling widespread pleiotropy.
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Affiliation(s)
- Elena Plekhanova
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Margarita A Vishnyakova
- Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - Sergey Bulyntsev
- Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - Peter L Chang
- Department of Plant Pathology, University of California, Davis, CA, USA.,Program Molecular and Computation Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Kassaye Negash
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Eric von Wettberg
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, USA
| | - Nina Noujdina
- School of Architecture, University of Southern California, Los Angeles, CA, USA
| | - Douglas R Cook
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Maria G Samsonova
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Sergey V Nuzhdin
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia. .,Program Molecular and Computation Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA.
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Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E, Oard J, Tohme J. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PLoS One 2015; 10:e0124617. [PMID: 25923345 PMCID: PMC4414565 DOI: 10.1371/journal.pone.0124617] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 03/02/2015] [Indexed: 01/08/2023] Open
Abstract
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.
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Affiliation(s)
- Jorge Duitama
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
- * E-mail:
| | - Alexander Silva
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
| | - Yamid Sanabria
- Rice Research Station, Louisiana State University Agricultural Center, Rayne, Louisiana, United States of America
| | - Daniel Felipe Cruz
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
| | - Constanza Quintero
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
| | - Carolina Ballen
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
| | - Mathias Lorieux
- 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
| | - Brian Scheffler
- 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
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Edgar Torres
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
| | - James Oard
- Rice Research Station, Louisiana State University Agricultural Center, Rayne, Louisiana, United States of America
| | - Joe Tohme
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
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Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD. Natural Selection in Gene-Dense Regions Shapes the Genomic Pattern of Polymorphism in Wild and Domesticated Rice. Mol Biol Evol 2011; 29:675-87. [DOI: 10.1093/molbev/msr225] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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