Genetics of seedling stage low temperature tolerance of rice

The world’s most important staple food is rice (Oryza sativa), which alone feeds more people than any other single crop. In South Asia, food security depends on the successful production of rice, but high population pressure and increased frequency of abiotic stresses associated with climate change, such as drought, flood, salinity and cold, threaten food security. As rice originated in tropical and subtropical regions, it is adapted to warm growing conditions, and low temperatures at the seedling stage can result in a wide range of negative effects. Due to global climate change, sudden episodes of low temperature now frequently affect many areas of Asia where such stresses to rice growth were previously rare. Therefore, the development of cultivars that are tolerant to low temperature at the seedling stage is expected to be one of the most effective and economical ways to improve rice production and especially the stability of rice production in areas that are prone to cold stress. To address this problem, three studies were conducted: (1) a comparison of new and previously published methods to screen rice seedlings for tolerance to low temperature, (2) a quantitative trait loci (QTL) analysis of two interconnected biparental populations, and (3), and a genome-wide association study (GWAS) on the japonica and basmati subset of the 3k rice genome project (3k RGP) panel (798 accessions phenotyped in this study). We hypothesized that using controlled environment chambers to mimick daily and weekly temperature variations of extremely cold years for rice growing areas that are prone to early season low temperatures would be more reliable and accurate for cold screening than short-duration, single-temperature stresses following warm germination and establishment common in standard protocols, as the mimicks better represent the real environment. With view of this, three treatment protocols were developed to mimic the cold seasons of two exceptionally cold years in Bangladesh. These three mimic protocol were tested with two previously published protocols along with two warm controls for assessing tolerance of rice seedlings to low temperature. Prior to screening in the mimic protocols, seeds were germinated at low temperature (20°C for 3 weeks), which was the mean temperature of that specific cold season for germination. In contrast, for previously published protocols seed were germinated at warm temperature (30°C for 1 week). Root and shoot growth during germination were very useful traits to evaluate tolerance to low temperature but germination proportion was not informative. For seedling stage screening, the mimic protocols showed important differences in growth potential in terms of height and dry biomass that were associated with low temperature, whereas such signals were largely absent from the standard protocols. QTLs that confer tolerance to low temperature in rice need to be identified and stacked in elite cultivars, then deployed to at-risk production fields. QTL mapping in two interconnected biparental populations was done to investigate genetic variation and identify genomic regions for seedling stage cold tolerance. A growth chamber trial was established at International Rice Research Institute for two BC1F5 populations derived from BR28*2/C21 and BR29*2/C21 challenged with 9°C for 14 days at the 3 leaf stage, where BR28 (BRRI dhan28) and BR29 (BRRI dhan29) are cold-sensitive indica mega-cultivars from Bangladesh, and C21 (C 21::IRGC 331-C1) is a cold-tolerant japonica cultivar. SNP genotyping was performed with an Illumina Infinium 7K SNP chip based on the MSU Rice Genome Annotation Project Release 7. Four QTL analysis methods for detecting marker-trait associations were compared: (1) single population single marker analysis (SMA) analysis, (2) single population composite interval mapping (CIM), (3) single population stepwise analysis, and (4) joint population stepwise analysis. These four methods detected 17, 21, 13 and 12 total QTLs. The identified SNPs associated with the QTLs for cold tolerance at seedling stage will be useful for introgressing desirable QTLs into cold-sensitive elite cultivars and can be used for pyramiding different QTLs for the development of rice cultivars with improved cold tolerance at the seedling stage. Lastly, a genome-wide association study on 798 accessions from the 3k RGP (including tropical japonica, temperate japonica, subtropical japonica, japonica admixed and basmati) was conducted by phenotyping in controlled environment chambers to investigate genetic variation and identify genomic regions for seedling stage cold tolerance. Genotyping was done with 4.8 million rice SNPs that were identified by aligning reads from the 3k RGP with the Nipponbare genome based on the MSU Rice Genome Annotation Project Release 7. This study identified nine QTL regions located on four chromosomes (1, 2, 11, and 12), which included 48 candidate genes, that were associated with low temperature tolerance at seedling stage. The identification of exceptionally tolerant accessions from the most cold tolerant subspecies of rice, and the QTLs linked to low temperature tolerance should facilitate the rapid development of new cold tolerant rice cultivars.U of I OnlyAuthor requested U of Illinois access only (OA after 2yrs) in Vireo ETD syste