Association mapping reveals multiple QTLs for grain protein content in rice useful for biofortification
- 41 Downloads
Rice is the staple food for majority of the global population. But, rice grain has low protein content (PC). Mapping of QTLs controlling grain PC is essential for enhancement of the trait through breeding programs. A shortlisted panel population for grain protein content was studied for genetic diversity, population structure and association mapping for grain PC. Phenotyping results showed a wide variation for grain PC. The panel population showed a moderate level of genetic diversity estimated through 98 molecular markers. AMOVA and structure analysis indicated linkage disequilibrium for grain PC and deviation of Hardy–Weinberg’s expectation. The analysis showed 15% of the variation among populations and 73% among individuals in the panel population. STRUCTURE analysis categorized the panel population into three subpopulations. The analysis also revealed a common primary ancestor for each subpopulation with few admix individuals. Marker-trait association using 98 molecular markers detected 7 strongly associated QTLs for grain PC by both MLM and GLM analysis. Three novel QTLs qPC3.1, qPC5.1 and qPC9.1 were detected for controlling the grain PC. Four reported QTLs viz., qPC3, QPC8, qPC6.1 and qPC12.1 were validated for use in breeding programs. Reported QTLs, qPC6, qPC6.1 and qPC6.2 may be same QTL controlling PC in rice. A very close marker RM407 near to protein controlling QTL, qProt8 and qPC8, was detected. The study provided clue for simultaneous improvement of PC with high grain yield in rice. The strongly associated markers with grain PC, namely qPC3, qPC3.1, qPC5.1, qPC6.1, qPC8, qPC9.1 and qPC12.1, will be useful for their pyramiding for developing protein rich high yielding rice.
KeywordsAssociation mapping Grain protein content Genetic diversity Population structure QTL mapping Linkage disequilibrium mapping
The authors thank Dr.SK Nayak former Editor-In-Chief, Oryza for checking the manuscript. They also thank Director, ICAR-National Rice Research Institute, Cuttack, Odisha for full support in providing facilities for the research work.
Conceived and designed the experiments: SKP EP. Performed the experiments: EP SP KC BB. Analysed the data: EP PD SS. Contributed reagents/materials/analysis tools: SKP JNR. Wrote the paper: SKP EP Editing: SKP JNR.
This research work was supported by ICAR-National Rice Research Institute, Cuttack, Odisha, India.
Compliance with ethical standards
Conflict of interest
All the authors declare that they have no competing interests.
Ethics approval and consent to participate
The authors declare that this study complies with the current laws of the country in which the experiments were performed. This article does not contain any studies with human participants or animals performed by any of the authors.
- Carnahan HL, Wiser WJ, Rutger JN (1972) Associations between protein content and other characters in rice (abstr.). In: Proc. 14th rice tech. working group, Univ. California, Davis. pp 31–32Google Scholar
- Coffman WR, Juliano BO (1987) Rice. In: Olson RA, Frey KJ (eds) Nutritional quality of cereal grains: genetic and agronomic improvement. Agronomy monograph no. 28, American Society of Agronomy, Madison, pp 101–131Google Scholar
- Faraji F, Esfahani M, Kavousi M, Nahvi M, Forghani A (2013) Effect of nitrogen fertilizer levels on Fe and protein content, grain breakage and grain yield of rice (Oryza sativa L. cv. Khazar). Biharean Biol 7(1):25–28Google Scholar
- Garris AJ, McCouch SR, Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165(2):759–769Google Scholar
- Gearing ME (2015) Good as gold: Can golden rice and other biofortified crops prevent malnutrition? Science in the News, Harvard University. http://sitn.hms.harvard.edu/
- HiileRisLambers D, Rutger JN, Qualset CO, Wiser WJ (1972) Heritability of protein content and its relationship to agronomic characters in rice. In: Proc. 14th rice tech. Working group, Univ. California, Davis. pp 31Google Scholar
- Mohanty A, Marndi BC, Sharma S, Das A (2011) Biochemical characterization of two high protein rice cultivars from Assam rice collections. Oryza 48(2):171–174Google Scholar
- NRRI Annual Report (2015) ICAR-national rice research institute (NRRI). Cuttack, IndiaGoogle Scholar
- Oko AO, Ubi BE, Efisue AA, Dambaba N (2012) Comparative analysis of the chemical nutrient composition of selected local and newly introduced rice varieties grown in ebonyi state of nigeria. Int J Agric For 2(2):16–23Google Scholar
- Pandit E, Tasleem S, Barik SR, Mohanty DP, Nayak DK, Mohanty SP, Das S, Pradhan SK (2017) Genome-wide association mapping reveals multiple qtls governing tolerance response for seedling stage chilling stress in indica rice. Front Plant Sci 8:552. https://doi.org/10.3389/fpls.2017.00552 CrossRefGoogle Scholar
- Patil AH, Premi V, Sahu V, Dubey M, Sahu GR, Chandel G (2014) Identification of elite rice germplasm lines for grain protein content, ssr based genotyping and dna fingerprinting. Int J Agric For 2(2):16–23Google Scholar
- Perrier X, Jacquemoud-Collet JP (2006) DARwin software available at http://darwin.cirad.fr/darwin
- Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959 (PMID: 10835412)Google Scholar
- Qin Y, Kim SM, Sohn JK (2009) QTL analysis of protein content in double-haploid lines of rice. Korean J Crop Sci 54(2):165–171Google Scholar
- Tan YF, Sun M, Xing YZ, Hua JP, Sun XL, Zhang QF, Corke H (2001) Mapping quantitative trait loci for milling quality, protein content and color characteristics of rice using a recombinant inbred line population derived from an elite rice hybrid. Theor Appl Genet 103(6,7):1037–1045CrossRefGoogle Scholar
- Uday G, Murthy MK, Hittalmani S (2014) Genetic analysis of recombinant inbred lines for total grain protein content and grain yeild in rice (oryza sativa l). Int J Agric Sci Res 4(2):51–58Google Scholar
- Yang Y, Guo M, Li R, Shen L, Wang W, Liu M, Zhu Q, Hu Z, He Q, Yang X, Tang S, Gu M, Yan C (2015) Identification of quantitative trait loci responsible for rice grain protein content using chromosome segment substitution lines and fine mapping of qPC-1 in rice (Oryza sativa L.). Mol Breed 35:130. https://doi.org/10.1007/s11032-015-0328-z CrossRefGoogle Scholar
- Zhang Y, Zou M, De T (2012) Association analysis of rice cold tolerance at tillering stage with SSR markers in Japonica cultivars in Northeast China. Chin J Rice Sci 26:423–430Google Scholar