qDTY12.1: a locus with a consistent effect on grain yield under drought in rice

BMC Genetics

Arvind Kumar²  Shailesh Marker¹  Paul Maturan²  Ma Teresa Sta Cruz²  Shalabh Dixit²  BP Mallikarjuna Swamy²  Ram Baran Yadaw³  Prashant Vikram²  Krishna Kumar Mishra³ 

[1] Sam Higginbottom Institute of Agriculture, Technology & Sciences, Allahabad 211007UP, India;International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines;Nepal Agricultural Research Council (NARC), Kathmandu, Nepal

关键词: QTL;    Rice;    Grain yield;    Drought;   

Others  :  1087333
DOI  :  10.1186/1471-2156-14-12

 received in 2012-09-05, accepted in 2013-02-22,  发布年份 2013

【 摘 要 】

Background

Selection for grain yield under drought is an efficient criterion for improving the drought tolerance of rice. Recently, some drought-tolerant rice varieties have been developed using this selection criterion and successfully released for cultivation in drought-prone target environments. The process can be made more efficient and rapid through marker-assisted breeding, a well-known fast-track approach in crop improvement. QTLs have been identified for grain yield under drought with large effects against drought-susceptible varieties. Most of the identified QTLs show large QTL × environment or QTL × genetic background interactions. The development of mapping populations in the background of popular high-yielding varieties, screening across environments, including the target environments, and the identification of QTLs with a consistent effect across environments can be a suitable alternative marker-assisted breeding strategy. An IR74371-46-1-1 × Sabitri backcross inbred line population was screened for reproductive-stage drought stress at the International Rice Research Institute, Philippines, and Regional Agricultural Research Station, Nepalgunj, Nepal, in the dry and wet seasons of 2011, respectively. A bulk segregant analysis approach was used to identify markers associated with high grain yield under drought.

Results

A QTL, qDTY_12.1, significantly associated with grain yield under reproductive-stage drought stress was identified on chromosome 12 with a consistent effect in two environments: IRRI, Philippines, and RARS, Nepalgunj, Nepal. This QTL explained phenotypic variance of 23.8% and contributed an additive effect of 45.3% for grain yield under drought. The positive QTL allele for qDTY_12.1 was contributed by tolerant parent IR74371-46-1-1.

Conclusions

In this study, qDTY_12.1 showed a consistent effect across environments for high grain yield under lowland reproductive-stage drought stress in the background of popular high-yielding but drought-susceptible recipient variety Sabitri. qDTY_12.1 was also reported previously [Crop Sci 47:507–516, 2007] to increase grain yield under upland reproductive-stage drought stress situations. qDTY_12.1 is the only QTL reported so far in rice to have shown a large effect against multiple recipient genetic backgrounds as well as under highly diverse upland and lowland rice ecosystems. qDTY_12.1 can be successfully introgressed to improve grain yield under drought of popular high-yielding but drought-susceptible lowland as well as upland adapted varieties following marker-assisted breeding.

【 授权许可】

   
2013 Mishra et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

【 参考文献 】

• [1]Pandey S, Bhandari H, Hardy B: Economic Costs of Drought and Rice Farmers’ Coping Mechanisms. A Cross-Country Comparative Analysis. Los Baños, Philippines/Singapore: International Rice Research Institute/World Scientific Publishing; 2007:1-9.
• [2]Huke RE, Huke EH: Rice area by type of culture: South, Southeast, and East Asia. Los Baños, Philippines: IRRI; 1997.
• [3]Evenson RE, Gollin D: Assessing the impact of the green revolution, 1960 to 2000. Science 2003, 300:758-762.
• [4]Vikram P, Swamy BPM, Dixit S, Ahmed HU, Sta Cruz MT, Singh AK, Kumar A: qDTY1.1, major QTL for rice GY under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genet 2011, 12:89.
• [5]Fukai S, Cooper M: Development of drought resistant cultivars using physio-morphological traits in rice. Field Crops Res 1995, 40:67-86.
• [6]Kumar A, Bernier J, Verulkar S, Lafitte HR, Atlin GN: Breeding for drought tolerance: direct selection for yield, response to selection and use of drought-tolerant donors in upland and lowland-adapted populations. Field Crops Res 2008, 107:221-231.
• [7]Venuprasad R, Lafitte HR, Atlin GN: Response to direct selection for grain yield under drought stress in rice. Crop Sci 2007, 47:285-293.
• [8]Kumar A, Verulkar SB, Mandal NP, Variar M, Shukla VD, Dwivedi JL, Singh BN, Singh ON, Swain P, Mall AK, Robin S, Chandrababu R, Jain A, Haefele SM, Piepho HP, Raman A: High- yielding, drought-tolerant, stable rice genotypes for the shallow rainfed lowland drought prone ecosystem. Field Crops Res 2012, 133:37-47.
• [9]Bernier J, Kumar A, Venuprasad R, Spaner D, Atlin GN: A large-effect QTL for GY under reproductive-stage drought stress in upland rice. Crop Sci 2007, 47:507-516.
• [10]Swamy BPM, Kumar A: Sustainable rice yield in water short drought prone environments: conventional and molecular approaches. In Irrigation systems and practices in challenging environments. Edited by Teang S. Janeza Trdine 9, 51000 Rijeka, Croatia: InTech; 2011:149-168.
• [11]Venuprasad R, Dalid CO, Del Valle M, Zhao D, Espiritu M, Sta Cruz MT, Amante M, Kumar A, Atlin GN: Identification and characterization of large-effect quantitative trait loci for GY under lowland drought stress in rice using bulk-segregant analysis. Theor Appl Genet 2009, 120:177-190.
• [12]Salekdeh GH, Siopongco J, Wade LJ, Ghareyazie B, Bennett J: A proteomic approach to analyzing drought and salt responsiveness in rice. Field Crops Res 2002, 76:199-219.
• [13]Ghimire KH, Quiatchon L, Vikram P, Swamy BPM, Dixit S, Ahmed HU, Hernandez JE, Borromeo TH, Kumar A: Identification and mapping of QTL (qDTY1.1) with a consistent effect on GY under RS. Field Crops Res 2012, 131:88-96.
• [14]Michelmoore RW, Paran I, Kesseli RV: Identification of markers linked to disease resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 1991, 88:9828-9832.
• [15]Murray MG, Thompson WF: Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 1980, 8:4321-4325.
• [16]Sambrook J, Fritsch EF, Maniatis T: Molecular cloning: a laboratory manual. 2nd edition. New York: Cold Spring Harbor; 1989.
• [17]Temnykh S, Declerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S: Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 2001, 11:1441-1452.
• [18]McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L: Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 2002, 9:199-207.
• [19]IRGSP: The map-based sequence of the rice genome. Nature 2005, 436:793-800.
• [20]Vikram P, Swamy BPM, Dixit S, Ahmed HU, Sta Cruz MT, Singh AK, Ye G, Kumar A: Bulk segregant analysis: An effective approach for mapping drought grain yield QTLs in rice. Field Crops Res 2012, 134:185-192.
• [21]Yang J, Zhu J, Williams RW: Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics 2007, 23:527-536.
• [22]Joehanes R, Nelson JC: QGene 4.0, an extensible java QTL-analysis platform. Bioinformatics 2008, 24:2788-2789.
• [23]Price AH, Cairns JE, Horton P, Jones RGW, Griffiths H: Linking drought-resistance mechanisms to drought avoidance in upland rice during a QTL approach: progress and new opportunities to integrate stomatal and mesophyll responses. J Exp Bot 2002, 53:989-1004.
• [24]Xing YZ, Tan YF, Hua JP, Sun XL, Xu CG, Zhang Q: Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet 2002, 105:248-257.
• [25]Verulkar SB, Mandal NP, Dwivedi JL, Singh BN, Sinha PK, Mahato RN, Swain P, Dongre P, Payasi D, Singh ON, Bose LK, Robin S, Babu RC, Senthil S, Jain A, Shashidhar HE, Hittalmani S, Vera Cruz C, Paris T, Hijmans R, Raman A, Haefele S, Serraj R, Atlin G, Kumar A: Breeding resilient and productive rice genotypes adapted to drought-prone rainfed ecosystems of India. Field Crops Res 2010, 117:197-208.
• [26]Bernier J, Kumar A, Spaner D, Verulkar S, Mandal NP, Sinha PK, Peeraju P, Dongre PR, Mahto RN, Atlin GN: Characterization of the effect of rice drought tolerance qtl12.1 over a range of environments in the Philippines and eastern India. Euphytica 2009, 166:207-217.
• [27]Babu RC, Nguyen BD, Chamarerk V, Shanmugasundaram P, Chezhian P, Jeyaprakash P, Ganesh SK, Palchamy A, Sadasivam S, Sarkarung S, Wade LJ, Nguyen HT: Genetic analysis of drought resistance in rice by molecular markers: association between secondary traits and field performance. Crop Sci 2003, 43:1457-1469.
• [28]Kumar R, Venuprasad R, Atlin GN: Genetic analysis of rainfed lowland rice drought tolerance under naturally-occurring stress in eastern India: heritability and QTL effects. Field Crops Res 2007, 103:42-52.
• [29]Swamy BPM, Vikram P, Dixit S, Ahmed HU, Kumar A: Meta-analysis of GY QTL identified during agricultural drought in grasses showed consensus. BMC Genomics 2011, 12:319. BioMed Central Full Text
• [30]Dixit S, Swamy BPM, Vikram P, Bernier J, Sta Cruz MT, Amante M, Atri D, Kumar A: Increased drought tolerance and wider adaptability of qDTY12.1 conferred by its interaction with qDTY2.3 and qDTY3.2. Mol Breed 2012, 30:1767-1779.
• [31]Kohli A, Narciso J, Oane R, Popluechai S, Kumar A: Identification of major candidate genes in a large effect QTL for rice yield under drought stress. [Paper presented at International Rice Congress, Hanoi, Vietnam, 9–11 November, 2010]
• [32]Biswal AK, Oane R, Raorane M, Narciso J, Blesilda AE, Kumar A, Kohli A: Identification of candidate genes in the large effect QTL DTY12.1 for yield under stress. [Presented at FCSSP Conference, held in Puerto Princesa City, Palawan, Philippines, April 16–21, 2012]