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Mapping Quantitative Trait Loci for Cold Tolerance in Rice at Seedling Stage

Nomita Das
Department of Botany, Jahangirnagar University, Savar, Dhaka-1340, Bangladesh

Nazmul Alam
Department of Botany, Jahangirnagar University, Savar, Dhaka-1340, Bangladesh

Kamal Hossain
Department of Botany, Jahangirnagar University, Savar, Dhaka-1340, Bangladesh

Partha S Biswas
Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur-1701, Bangladesh.

Abstract/ Executive Summary:

Rice plants are sensitive to cold stress at various growth stages starting from germination to maturity. Exploitation of cold tolerance for the development of cold tolerant varieties may help in saving crop loss or cost of production in the cold prone environment. Introgression of quantitative trait loci (QTLs) conferring cold tolerance in the elite variety may be the most effective and sustainable approach to address this issue. A F_2:3 mapping population of a cross between a cold susceptible variety (BR1) and a cold tolerant variety (BR18) was used to map QTLs for cold tolerance at seedling stage. Three significant QTLs on chromosomes 1, 3 and 12 associated with cold tolerance were mapped between the markers intervals of RM220-RM10829, RM546-RM7 and RM27877-RM463, respectively at a threshold LOD of 4.3 through composite interval mapping. Phenotypic contributions of these QTLs were 50.7, 39 and 52.7%, respectively. Marker information of such a large effect QTL could be used in the breeding program after necessary validation to develop cold tolerant high yielding rice varieties.

Keywords: Quantitative trait loci, Cold tolerance, Seedling stage, Rice

Location: Plant Breeding Division of Bangladesh Rice Research Institute, Gazipur, Bangladesh

Start Date:

End Date:

Program Area: Crop-Soil-Water Management

Commodity: Rice

Objectives:

This study was undertaken to map QTLs from a F_2:3 mapping population of BR1 × BR18.

Methodology:

A set of 856 F_2:3 mapping population derived from a cross between BR1 and BR18 was used for this study. All the field and laboratory work for this study were conducted at Plant Breeding Division of Bangladesh Rice Research Institute, Gazipur, Bangladesh in collaboration with Department of Botany, Jahangirnagar University, Savar, Dhaka, Bangladesh. BR1 is a cold susceptible high yielding variety at seedling stage. On the other hand, BR18 is cold tolerant rice variety at seedling stage. Although BR18 is a high yielding variety developed by BRRI for Haor regions of the country, its tall stature does not fit to the cold prone northern districts of Bangladesh. The F_2:3 progenies were evaluated for cold tolerance using cold treatment of constant 13°C in a cold-water tank following Khatun et al. (2016). Briefly, seeds were sown in plastic trays filled with gravels and crop residue free granular soil with 3 replicates. Ten seedlings of each entry were raised at ambient temperature at each replication. At three-leaf stage (12 - 14 days after seeding), the plastic trays were placed in cold water tanks preset at 13°C. The depth of water in the tank was maintained at 5 cm. Temperature of cold water tank was kept at constant 13°C for 6 days or until the susceptible check variety dies. An arbitrary leaf discoloration (LD) scores (1 to 9; 1 means all leaves are green and 9 means seedlings are almost dead) was assigned to each entry considering magnitude of discoloration of leaves due to low temperature treatment on the day of LD scoring following standard evaluation system (SES) of IRRI (IRRI 2013). Parental polymorphism information of around 560 SSR markers distributed over rice genome for BR1 and BR18 was analyzed using method described by Syed et al. (2016). Briefly, DNA was extracted from young and actively growing fresh leaves using miniprep modified CTAB method. Polymerase chain reaction (PCR) was performed in 10 µl volume containing 2 µl of genomic DNA, 5.3 µl of DDH₂O, 1 µl of 1X PCR buffer, 1 µl of 0.1mM dNTP mix, 0.5 µl of 0.25 µM of each primer, 2 µl of Taq polymerase of 1U. The temperature cycles were programmed at 94°C for 5 min (initial denaturation), 94°C for 30 sec (denaturation), 55°C for 30 sec (primer annealing), 72°C for 60 sec (extension), 72°C for 5 min (final extension) and 10°C forever (storage). The PCR product was separated on 6% polyacrylamide gel through electrophoresis for 1.5 to 2.5 hrs and was visualized in a gel documentation system. Parental polymorphism was determined based on the comparative deviation in band position. Selective genotyping technique (Lander and Botstein 1989) was used to select plants for genotyping. A set of 40 F₂ plants along with their parents were used in genotyping with 76 polymorphic SSR markers distributed over 12 chromosomes of rice. Allele scoring was performed based on comparative position of the parental DNA bands. The progeny having band at same level of BR18’s band was scored as ‘A’ and the progeny having band at same level of BR1’s band was scored as ‘B’ while heterozygous alleles were scored as ‘H’. Construction of linkage map and detection of QTLs for cold tolerance were performed using QGene4.0 (Nelson 1997). Each marker was analyzed through single marker analysis (SMA). To be more precise about the location of the identified QTLs, interval mapping (IM) and composite interval mapping (CIM) analysis were performed. Permutation test was performed with 1000 interations to declar threshold LOD (Logarithm of Odds) for significant QTL at 5% level of probability. The proportion of the total phenotypic variation explained by each QTL was calculated as R² value (R² = Ratio of the sum of squares explained by the QTL to the total sum of squares). The QTLs were named based on the nomenclature suggested by McCouch et al. (1997).

Source of Information: Bangladesh J. Bot. 48(4): 1021-1028, 2019 (December)

Article Link (Online Journal): DOI: https://doi.org/10.3329/bjb.v48i4.49050

Funding Source:

Budget:

Total Budget (Tk.) :

Achievement/Findings:

The identified QTLs, qCTS1.1, qCTS3 and qCTS12 were found tightly linked with RM490, RM218 and RM1261, respectively. The qCTS1.1 and qCTS3 showed negative additive effects while qCTS12 showed positive value, which indicated that the favorable alleles of the former two QTLs for cold tolerance were inherited from donor parent BR18 and that of latter was arisen from susceptible parent BR1.

Knowledge Management: Journal