Abstract
There is a steady demand for high-quality rice varieties though consumers’ preference for high-quality rice varies from regions. The improvement of the quality of rice, especially its eating and cooking quality (ECQ), is an important breeding target as rice is mainly consumed in cooked form. The development and utilization of breeder-friendly and high-throughput marker systems play a pivotal role in marker-assisted breeding of rice cultivars, with pyramids of valuable genes affecting rice ECQ. In this study, we developed functional markers based on the Kompetitive Allele-Specific PCR (KASP) method for three principal genes, Wx, BADH2 and ALK, affecting ECQ in rice. The accuracy of all KASP markers was verified and confirmed with Sanger sequencing. A diverse rice panel consisting of 38 indica cultivars, 9 japonica cultivars and 1 Javanica cultivar were used to assess the validity of these markers for genotyping. The results showed that the functional KASP markers of Wx, ALK and BADH2 could effectively distinguish the different alleles. The genotyping results highly coincided with the phenotypic traits of rice eating and cooking quality. Eight rice entries harboring 3 favorable alleles were identified and superior rice restorers with improved ECQ were bred via functional marker genotyping. Breeders can develop rice cultivars that have desirable ECQ, customized to meet the market requirements in target regions. Hence, the development of these 3 applicable KASP functional markers based on allelic variation would be valuable for improving rice eating and cooking quality through maker-assisted selection to carter various consumer preferences especially in Asian areas.
Similar content being viewed by others
References
Bao JS, Corke H, Sun M (2006) Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.). Theor Appl Genet 113:1171–1183
Bradbury LMT, Fitzgerald TL, Henry RJ, Jin QS, Waters DLE (2005) The gene for fragrance in rice. Plant Biotechnol J 3:363–370
Bunyasiri IN, Sirisupluxana P (2018) Consumer’s behavior and rice attributes for Thai HomMali Rice in Sichuan Province of China. J Bus Retail Manag Res 12:242–252
Cai XL, Wang ZY, Xing YY, Zhang JL, Hong MM (1998) Aberrant splicing of intron 1 leads to the heterogeneous 5’ UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content. Plant J 14:459–465
Calingacion M et al (2014) Diversity of global rice markets and the science required for consumer-targeted rice breeding. PLoS ONE 9:e85106. https://doi.org/10.1371/journal.pone.0085106
Chen SH et al (2008) Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell 20:1850–1861
Chen T, Zhang Y, Zhao L, Zhu Z, Lin J, Zhang S, Wang C (2009) A cleaved amplified polymorphic sequence marker to detect variation in Wx locus conditioning translucent endosperm in rice. Rice Sci 16:106–110
Chen W et al (2014) Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nat Genet 46:714–721
Gao Z et al (2003) Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice. Sci China C Life Sci 46:661–668
He C, Holme J, Anthony J (2014) SNP genotyping: the KASP assay. Methods Mol Biol 1145:75–86. https://doi.org/10.1007/978-1-4939-0446-4_7
Kharabian-Masouleh A, Waters DLE, Reinke RF, Ward R, Henry RJ (2012) SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Sci Rep 2:557
Leng YJ et al (2014) Mapping of QTLs for eating and cooking quality-related traits in rice (Oryza sativa L.). Euphytica 197:99–108
Luo WL, Guo T, Yang QY, Wang H, Liu YZ, Zhu XY, Chen ZQ (2014) Stacking of five favorable alleles for amylase content, fragrance and disease resistance into elite lines in rice (Oryza sativa) by using four HRM-based markers and a linked gel-based marker. Mol Breed 34:805–815
Ma Y et al (2017) Development and validation of breeder-friendly KASPar markers for er1, a powdery mildew resistance gene in pea (Pisum sativum L.). Mol Breed 37:151. https://doi.org/10.1007/s11032-017-0740-7
Musa M, Othman N, Fatah AF (2018) Determinants of consumers purchasing behavior for rice in Malaysia. Am Int J Contemp Res 1:159–167
Myakishev MV, Khripin Y, Hu S, Hamer DH (2001) High-throughput SNP genotyping by allele-specific PCR with universal energy-transfer-labeled primers. Genome Res 11:163–169
Neelam K, Brown-Guedira G, Huang L (2013) Development and validation of a breeder-friendly KASPar marker for wheat leaf rust resistance locus Lr21. Mol Breed 31:233–237. https://doi.org/10.1007/s11032-012-9773-0
Pang YL, Ali J, Wang XQ, Franje NJ, Revilleza JE, Xu JL, Li ZK (2016) Relationship of rice grain amylose, gelatinization temperature and pasting properties for breeding better eating and cooking quality of rice varieties. PLoS ONE 11:e0168483. https://doi.org/10.1371/journal.pone.0168483
Ramkumar G, Prahalada GD, Hechanova SL, Vinarao R, Jena KK (2015) Development and validation of SNP-based functional codominant markers for two major disease resistance genes in rice (O. sativa L.). Mol Breed 35:129
Sakthivel K et al (2009) Development of a simple functional marker for fragrance in rice and its validation in Indian Basmati and non-Basmati fragrant rice varieties. Mol Breed 24:185–190. https://doi.org/10.1007/s11032-009-9283-x
Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14
Su Y et al (2011) Map-based cloning proves qGC-6, a major QTL for gel consistency of japonica/indica cross, responds by Waxy in rice (Oryza sativa L.). Theor Appl Genet 123:859–867
Sun YY, Lv Y, Dong CL, Wang PR, Huang XQ, Deng XJ (2005) Genetic relationship among Wx gene, AC, GC and GT of rice. Acta Agron Sin 31:535–539
Sun MM, Abdula SE, Lee HJ, Cho YC, Han LZ, Koh HJ, Cho YG (2011) Molecular aspect of good eating quality formation in Japonica rice. PLoS ONE 6:e18385. https://doi.org/10.1371/journal.pone.0018385
Thomson M (2014) High-throughput SNP genotyping to accelerate crop improvement. Plant Breed Biotechnol 2:195–212
Tian ZX et al (2010) Development of gene-tagged molecular markers for starch synthesis-related genes in rice. Chin Sci Bull 55:3768–3777
Tong C, Chen Y, Tang F, Xu F, Huang Y, Chen H, Bao J (2014) Genetic diversity of amylose content and RVA pasting parameters in 20 rice accessions grown in Hainan, China. Food Chem 161:239–245. https://doi.org/10.1016/j.foodchem.2014.04.011
Tuano A, Regalado M, Juliano B (2016) Grain quality of rice in selected retail stores and supermarkets in the Philippines. J Philipp Sci Techol 9:15–22
Umemoto T, Aoki N (2005) Single-nucleotide polymorphisms in rice starch synthase IIa that alter starch gelatinisation and starch association of the enzyme. Funct Plant Biol 32:763–768
Wang H, Chu Z, Ma X, Li R, Liu Y (2013) A high through-put protocol of plant genomic DNA preparation for PCR. Acta Agron Sin 39:1200–1205
Waters DLE, Henry RJ, Reinke RF, Fitzgerald MA (2006) Gelatinization temperature of rice explained by polymorphisms in starch synthase. Plant Biotechnol J 4:115–122
Yang F et al (2014) Association mapping of starch physicochemical properties with starch synthesis-related gene markers in nonwaxy rice (Oryza sativa L.). Mol Breed 34:1747–1763. https://doi.org/10.1007/s11032-014-0135-y
Zhang ZJ et al (2012) Diversification of the waxy gene is closely related to variations in rice eating and cooking quality. Plant Mol Biol Report 30:462–469
Acknowledgements
Financial support for this research was provided in part by a grant from the National Key Research and Development Project (2016YFD0101100), Science and Technology Project of Guangdong Province (No. 2015B020231011), National Key Technology Research and Development Program of China (No. 2016YFD0102102), and the earmarked fund for Modern Agro-Industry Technology Research System (No. CARS-01-12).
Author information
Authors and Affiliations
Corresponding authors
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Yang, G., Chen, S., Chen, L. et al. Development and utilization of functional KASP markers to improve rice eating and cooking quality through MAS breeding. Euphytica 215, 66 (2019). https://doi.org/10.1007/s10681-019-2392-7
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s10681-019-2392-7