TY - JOUR
T1 - Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems
AU - Wade, Len J.
AU - Bartolome, Violeta
AU - Mauleon, Ramil
AU - Vasant, Vivek Deshmuck
AU - Prabakar, Sumeet Mankar
AU - Chelliah, Muthukumar
AU - Kameoka, Emi
AU - Nagendra, K.
AU - Reddy, K. R. Kamalnath
AU - Varma, C. Mohan Kumar
AU - Patil, Kalmeshwar Gouda
AU - Shrestha, Roshi
AU - Al-Shugeairy, Zaniab
AU - Al-Ogaidi, Faez
AU - Munasinghe, Mayuri
AU - Gowda, Veeresh
AU - Semon, Mande
AU - Suralta, Roel R.
AU - Shenoy, Vinay
AU - Vadez, Vincent
AU - Serraj, Rachid
AU - Shashidhar, H. E.
AU - Yamauchi, Akira
AU - Babu, Ranganathan Chandra
AU - Price, Adam
AU - McNally, Kenneth L.
AU - Henry, Amelia
N1 - Funding: This research was funded by the Generation Challenge Program (GCP) project G3008.06, “Targeting Drought-Avoidance Root Traits to Enhance Rice Productivity under Water-Limited Environments". The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
PY - 2015/4/24
Y1 - 2015/4/24
N2 - The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers) was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E) component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7-40.7 Mb) and on chromosome 8 (20.3-21.9 Mb). Across experiments, the soil type/growth medium showed more correlations with plant growth than the container dimensions. Although the correlations among studies and genetic co-location of root traits from a range of study systems points to their potential utility to represent responses in field studies, the best correlations were observed when the two setups had some similar properties. Due to the co-location of the identified genomic regions (from introgression block analysis) with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought. This study also highlights the utility of characterizing a small set of 20 genotypes for root growth, drought response, and related genomic regions.
AB - The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers) was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E) component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7-40.7 Mb) and on chromosome 8 (20.3-21.9 Mb). Across experiments, the soil type/growth medium showed more correlations with plant growth than the container dimensions. Although the correlations among studies and genetic co-location of root traits from a range of study systems points to their potential utility to represent responses in field studies, the best correlations were observed when the two setups had some similar properties. Due to the co-location of the identified genomic regions (from introgression block analysis) with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought. This study also highlights the utility of characterizing a small set of 20 genotypes for root growth, drought response, and related genomic regions.
KW - QUANTITATIVE TRAIT LOCI
KW - FED LOWLAND CONDITIONS
KW - SOIL-FILLED CHAMBERS
KW - SATIVA L.
KW - GRAIN-YIELD
KW - PENETRATION ABILITY
KW - WATER-DEFICIT
KW - MORPHOLOGICAL TRAITS
KW - GENETIC BACKGROUNDS
KW - ALUMINUM TOLERANCE
U2 - 10.1371/journal.pone.0124127
DO - 10.1371/journal.pone.0124127
M3 - Article
SN - 1932-6203
VL - 10
JO - PloS ONE
JF - PloS ONE
IS - 4
M1 - 0124127
ER -