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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #337075

Title: Assessment of five cold chilling tolerance traits and GWAS mapping in rice using the USDA mini-core collection

item SCHLAPPI, MICHAEL - Marquette University
item Jackson, Aaron
item Eizenga, Georgia
item WANG, AIJU - Chinese Academy Of Sciences
item CHU, CHENGCAI - Chinese Academy Of Sciences
item SHI, YAO - Marquette University
item SHIMOYAMA, NAOKI - Marquette University
item Boykin, Deborah

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/22/2017
Publication Date: 6/8/2017
Citation: Schlappi, M.R., Jackson, A.K., Eizenga, G.C., Wang, A., Chu, C., Shi, Y., Shimoyama, N., Boykin, D.L. 2017. Assessment of five cold chilling tolerance traits and GWAS mapping in rice using the USDA mini-core collection. Frontiers in Plant Science. doi:10.3389/fpls.2017.00957.

Interpretive Summary: Improved cold tolerance in rice is needed both at the germination and seedling stages. Improved tolerance at the germination stage would allow rice to be planted directly into the fields earlier in the spring and allow the crop to take advantage of the spring rains, especially in the southern United States. Improved cold tolerance during the seedling stage would permit better survival when transplanting into cool water originating from mountain reservoirs or when flooding fields with cold water after the seedlings were at the four-leaf stage. Cold tolerance at the seedling stage also provides protection from unexpected cold temperatures that occur post germination. Using a set of over 200 rice varieties from around the world, five different assays were conducted to mimic cold conditions at the germination stage or at the seedling stage. At germination, the two scenarios were cool temperatures either during or shortly after the seed had germinated. At the seedling stage, the three scenarios examined were cold temperatures occurring at transplanting, soon after transplanting, or after the seed had germinated and grown to the seedling stage. Based on the five assays and analyses with DNA markers, 27 chromosomal regions were discovered where genes controlling cold tolerance at germination or the seedling stage were located. Each region was identified by a DNA marker and all but one region had been previously reported by other research groups. This study will provide the foundation for identifying rice varieties in this global collection that can be used by rice breeders to incorporate cold tolerance into adapted varieties along with DNA markers to identify the cold tolerance in new rice varieties. Based on these results, additional studies will be conducted to understand the basic biological mechanisms controlling cold tolerance at the germination and seedling stages in rice.

Technical Abstract: Rice (Oryza sativa L.) is often exposed to cool or cold temperatures during spring planting in a temperate climate. A better understanding of the genetic pathways regulating this chilling tolerance will enable breeders to develop varieties with improved tolerance during the germination and young seedling stages. To dissect cold tolerance, five assays were developed; two assays for the germination stage and three for the seedling stage. Based on these assays, five cold tolerance indices were calculated and assessed using 202 O. sativa accessions from the Rice Mini-Core (RMC) collection. Significant differences between RMC accessions made the five indices suitable for genome-wide association (GWA) quantitative trait loci (QTL) mapping. For young seedling stage indices, japonica and indica subspecies clustered into cold tolerant and cold sensitive accessions, respectively, while both subspecies had similar low temperature germinability distributions. GWA mapping with 157 DNA markers, uncovered 33 QTL at 27 chromosome regions distributed across 11 of the 12 rice chromosomes. Interestingly, there was no overlap between the germination and seedling stage QTL. Also, 26 QTL were in regions discovered in previously reported bi-parental or GWA QTL studies. Only, the novel low temperature seedling survivability (LTSS)–QTL, qLTSS4-1, was not in a previously reported QTL region. Some of the QTL identified in this study will be useful for future marker assisted breeding efforts to improve cold tolerance in rice cultivars and cold tolerance gene discovery.