1
|
McDiarmid CS, Friesen CR, Ballen C, Olsson M. Sexual coloration and sperm performance in the Australian painted dragon lizard,
Ctenophorus pictus. J Evol Biol 2017; 30:1303-1312. [DOI: 10.1111/jeb.13092] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/12/2017] [Indexed: 12/16/2022]
Affiliation(s)
- C. S. McDiarmid
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - C. R. Friesen
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - C. Ballen
- College of Biological Sciences University of Minnesota Minneapolis MN USA
| | - M. Olsson
- Department of Biological and Environmental Sciences Göteborg University Göteborg Sweden
| |
Collapse
|
2
|
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: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
3
|
Fory PA, Triplett L, Ballen C, Abello JF, Duitama J, Aricapa MG, Prado GA, Correa F, Hamilton J, Leach JE, Tohme J, Mosquera GM. Comparative analysis of two emerging rice seed bacterial pathogens. Phytopathology 2014; 104:436-444. [PMID: 24261408 DOI: 10.1094/phyto-07-13-0186-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Seed sterility and grain discoloration limit rice production in Colombia and several Central American countries. In samples of discolored rice seed grown in Colombian fields, the species Burkholderia glumae and B. gladioli were isolated, and field isolates were compared phenotypically. An artificial inoculation assay was used to determine that, although both bacterial species cause symptoms on rice grains, B. glumae is a more aggressive pathogen, causing yield reduction and higher levels of grain sterility. To identify putative virulence genes differing between B. glumae and B. gladioli, four previously sequenced genomes of Asian and U.S. strains of the two pathogens were compared with each other and with two draft genomes of Colombian B. glumae and B. gladioli isolates generated for this study. Whereas previously characterized Burkholderia virulence factors are highly conserved between the two species, B. glumae and B. gladioli strains are predicted to encode distinct groups of genes encoding type VI secretion systems, transcriptional regulators, and membrane-sensing proteins. This study shows that both B. glumae and B. gladioli can threaten grain quality, although only one species affects yield. Furthermore, genotypic differences between the two strains are identified that could contribute to disease phenotypic differences.
Collapse
|