title: Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems.
abstract: 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.
authors.affiliation: Charles Sturt University, Graham Centre for Agricultural Innovation, Locked Bag 588, Wagga Wagga, New South Wales, 2678, Australia.
authors.forename: Len J
authors.initials: LJ
authors.lastname: Wade
authors.affiliation: International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, 1301, Philippines.
authors.forename: Violeta
authors.initials: V
authors.lastname: Bartolome
authors.affiliation: International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, 1301, Philippines.
authors.forename: Ramil
authors.initials: R
authors.lastname: Mauleon
authors.affiliation: Center for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India.
authors.forename: Vivek Deshmuck
authors.initials: VD
authors.lastname: Vasant
authors.affiliation: Center for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India.
authors.forename: Sumeet Mankar
authors.initials: SM
authors.lastname: Prabakar
authors.affiliation: Center for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India.
authors.forename: Muthukumar
authors.initials: M
authors.lastname: Chelliah
authors.affiliation: Graduate School of Bioagricultural Sciences, Nagoya University Chikusa, Nagoya, 464-8601, Japan.
authors.forename: Emi
authors.initials: E
authors.lastname: Kameoka
authors.affiliation: Barwale Foundation, Barwale Chambers, Street No.10, Himayat nagar, Hyderabad, 500029, India.
authors.forename: K
authors.initials: K
authors.lastname: Nagendra
authors.affiliation: Barwale Foundation, Barwale Chambers, Street No.10, Himayat nagar, Hyderabad, 500029, India.
authors.forename: K R Kamalnath
authors.initials: KR
authors.lastname: Reddy
authors.affiliation: Barwale Foundation, Barwale Chambers, Street No.10, Himayat nagar, Hyderabad, 500029, India.
authors.forename: C Mohan Kumar
authors.initials: CM
authors.lastname: Varma
authors.affiliation: Barwale Foundation, Barwale Chambers, Street No.10, Himayat nagar, Hyderabad, 500029, India.
authors.forename: Kalmeshwar Gouda
authors.initials: KG
authors.lastname: Patil
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom.
authors.forename: Roshi
authors.initials: R
authors.lastname: Shrestha
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom.
authors.forename: Zaniab
authors.initials: Z
authors.lastname: Al-Shugeairy
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom.
authors.forename: Faez
authors.initials: F
authors.lastname: Al-Ogaidi
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom.
authors.forename: Mayuri
authors.initials: M
authors.lastname: Munasinghe
authors.affiliation: International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, 1301, Philippines.
authors.forename: Veeresh
authors.initials: V
authors.lastname: Gowda
authors.affiliation: Africa Rice Center, c/o IITA, PMB 5320 Oyo Road, Ibadan, Nigeria.
authors.forename: Mande
authors.initials: M
authors.lastname: Semon
authors.affiliation: Philippine Rice Research Institute, Maligaya, Science City of Muñoz, 3119, Nueva Ecija, Philippines.
authors.forename: Roel R
authors.initials: RR
authors.lastname: Suralta
authors.affiliation: Barwale Foundation, Barwale Chambers, Street No.10, Himayat nagar, Hyderabad, 500029, India.
authors.forename: Vinay
authors.initials: V
authors.lastname: Shenoy
authors.affiliation: International Crops Research Institute for the Semi-Arid-Tropics (ICRISAT), Patancheru, Telangana, 502324, India.
authors.forename: Vincent
authors.initials: V
authors.lastname: Vadez
authors.affiliation: International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, 1301, Philippines.
authors.forename: Rachid
authors.initials: R
authors.lastname: Serraj
authors.affiliation: College of Agriculture, University of Agricultural Sciences-Gandhi Krishi Vignana Kendra (GKVK), Bangalore, 560065, India.
authors.forename: H E
authors.initials: HE
authors.lastname: Shashidhar
authors.affiliation: Graduate School of Bioagricultural Sciences, Nagoya University Chikusa, Nagoya, 464-8601, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Yamauchi
authors.affiliation: Center for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India.
authors.forename: Ranganathan Chandra
authors.initials: RC
authors.lastname: Babu
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom.
authors.forename: Adam
authors.initials: A
authors.lastname: Price
authors.affiliation: International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, 1301, Philippines.
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: McNally
authors.affiliation: International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, 1301, Philippines.
authors.forename: Amelia
authors.initials: A
authors.lastname: Henry
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D055864:Droughts; D004777:Environment; D056726:Genetic Association Studies; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics* / Q000254:growth & development*; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci