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Genotyping USDA rice (Oryza spp.) mini-core collection with functional markers for important agronomic traits

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Abstract

The USDA rice mini-core collection was established to capture the diversity of an entire collection of over 18,700 accessions of global origins for efficient germplasm evaluation and exploration. Previous studies have investigated its genetic diversity and population structure using genome-wide SSR markers. Many important agronomic traits that are fundamental to rice breeding programs, however, remain to be explored. Functional markers can be developed based on polymorphic sites within genes affecting phenotypic variation in, e.g., starch physicochemical properties, nutritional qualities and biotic resistance. These markers can be used for genotyping and hence differentiating phenotypes among rice accessions. In this study, we employed 12 pairs of functional markers (SNP and Indel) to genotype all 217 accessions constituting the USDA rice mini-core. These markers are highly associated with starch physicochemical properties (intron 1 G/C SNP, 23 bp duplication in exon 2, exon 6 C/A SNP, exon 10 C/T SNP of Waxy gene, GC/TT SNPs of SSIIa gene, G/C SNP of SBE3 gene), glutelin content (3.5 kb deletion in Lgc1 gene), grain length (C/A SNP in GS3 gene), brown planthopper resistance (InDel in Bph 14 gene) and rice blast resistance (InDel in Pi54 and Pit gene). Using these functional markers, all the 217 accessions of the mini-core are characterized for aforementioned agronomic traits associated alleles/genes. The results of this study will help breeders select parental materials with desirable allele/gene combinations and phenotypes among mini-core accessions for rice breeding programs.

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References

  • Agrama HA, Yan WG, Lee F, Fjellstrom R, Chen MH, Jia M, McClung A (2009) Genetic assessment of a mini-core subset developed from the USDA rice genebank. Crop Sci 49:1336–1346

    Article  Google Scholar 

  • Anderson JR, Lubberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560

    Article  CAS  Google Scholar 

  • Ayers NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germ plasm. Theor Appl Genet 94:773–781

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Bassam BJ, Anolles GC, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83

    Article  CAS  PubMed  Google Scholar 

  • Bligh HFJ, Larkin PD, Roach PS, Jones CA, Fu H, Park WD (1998) Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties. Plant Mol Biol 38:407–415

    Article  CAS  PubMed  Google Scholar 

  • Bryant RJ, Jackson AK, Yeaster KM, Yan WG, McClung AM, Fjellstrom RG (2013) Genetic variation and association mapping of protein concentration in brown rice using a diverse rice germplasm collection. Cereal Chem 90(5):445–452

    Article  CAS  Google Scholar 

  • Caffagni A, Albertazzi G, Gavina G, Ravaglia S, Gianinetti A, Pecchioni N, Milc J (2013) Characterization of an Italian rice germplasm collection with genetic markers useful for breeding to improve eating and cooking quality. Euphytica 194:383–399

    Article  CAS  Google Scholar 

  • Cai XL, Wang ZY, Xing YY, Zhang JL, Hong MM (1998) Aberrent 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(4):459–465

    Article  CAS  PubMed  Google Scholar 

  • Chen MH, Bergman CJ, Pinson SRM, Fjiellstrom RG (2008) Waxy gene haplotypes: associations with pasting properties in an international rice germplasm collection. J Cereal Sci 48(3):781–788

    Article  CAS  Google Scholar 

  • Chen T, Tian MX, Zhang YD, Zhu Z, Zhao L, Zhao QY, Lin J, Zhou LH, Wang CL (2010) Development of simple functional markers for low glutelin content gene 1 (Lgc1) in rice (Oryza sativa). Rice Sci 17(3):173–178

    Article  Google Scholar 

  • Doyle JJ (1991) DNA protocols for plants-CTAB total DNA isolation. In: Hewitt GM (ed) Molecular techniques in taxonomy. Springer, Berlin, pp 283–293

    Chapter  Google Scholar 

  • Du B, Zhang WL, Liu BF, Hu J, Wei Z, Shi ZY, He RF, Zhu LL, Chen RZ, Han B et al (2009) Identification and characterization of Bph14, a gene conferring resistance to brown planthopper in rice. Proc Natl Acad Sci USA 52:22163–22168

    Article  Google Scholar 

  • Ellis MH, Spielmeyer W, Gale KR, Rebetzke GJ, Richards RA (2002) “Perfect” markers for the Rht-B1b and Rht-D1b dwarfing genes in wheat. Theor Appl Genet 105:1038–1042

    Article  CAS  PubMed  Google Scholar 

  • Fan CC, Xing YZ, Mao HL, Lu TT, Han B, Xu CG, Li XH, Zhang QF (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171

    Article  CAS  PubMed  Google Scholar 

  • Fan CC, Yu SB, Wang CG, Xing YZ (2009) A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. Theor Appl Genet 118:465–472

    Article  CAS  PubMed  Google Scholar 

  • Fujita N, Kubo A, Suh DS, Wong KS, Jane JL, Ozawa K, Takaiwa F, Inaba Y, Nakamura Y (2003) Antisense inhibition of isoamylase alters structure of amylopectin and the physicochemical properties of starch in rice endosperm. Plant Cell Physiol 44(6):607–618

    Article  CAS  PubMed  Google Scholar 

  • Garris AJ, McCouch SR, Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding xa5 locus of rice (Oryza sativa L.). Genetics 165:759–769

    Article  PubMed  PubMed Central  Google Scholar 

  • Han YP, Xu ML, Liu XY, Yan CJ, Korban SS, Chen XL, Gu MH (2004) Genes coding for starch branching enzymes are major contributors to starch viscosity characteristics in waxy rice (Oryza sativa L.). Plant Sci 166:357–364

    Article  CAS  Google Scholar 

  • Hayashi K, Yasuda N, Fujita Y, Koizumi S, Yoshida H (2010) Identification of the blast resistance gene Pit in rice cultivars using functional markers. Theor Appl Genet 121:1357–1367

    Article  CAS  PubMed  Google Scholar 

  • Hirano HY, Eiguchi M, Sano Y (1998) A single base change altered theregulation of the Waxy gene at the post-transcriptional level druing the domestication of rice. Mol Biol Evol 15:978–987

    Article  CAS  PubMed  Google Scholar 

  • Hizukuri S, Abe JI, Hanashiro I (2006) Starch: analytical aspects. In: Eliasson AC (ed) Carbohydrates in food, 2nd edn. CRC Press, Boca Raton, pp 305–390

    Google Scholar 

  • Huang Z, He GC, Shu LH, Li XH, Zhang QF (2001) Identification and mapping of two brown planthopper resistance genes in rice. Theor Appl Genet 102:929–934

    Article  CAS  Google Scholar 

  • Iida S, Amano E, Nishio T (1993) A rice (Oryza sativa L.) mutant having a low content of glutelin and a high content of prolamine. Theor Appl Genet 87(3):374–378

  • Iida S, Kusaba M, Nishio T (1997) Mutants lacking glutelin subunits in rice: mapping and combination of mutated glutelin genes. Theor Appl Genet 94(2):177–183

    Article  CAS  Google Scholar 

  • Isshiki M, Morino K, Nakajima M, Okagaki RJ, Wessler SR, Izawa T, Shimamoto K (1998) A naturally occurring functional allele of the waxy locus has a GT to TT mutation at the 5′ splice of the first intron. Plant J 15:133–138

    Article  CAS  PubMed  Google Scholar 

  • Iyer-Pascuzzi AS, McCouch SR (2007) Functional markers for xa5-mediated resistance in rice (Oryza sativa L.). Mol Breed 19:291–296

    Article  CAS  Google Scholar 

  • Jairin J, Sansen K, Wongbong W, Kothcharerk J (2010) Detection of a brown planthopper resistance gene bhp4 at the same chromosomal position of Bph3 using two different genetic backgrounds of rice. Breed Sci 60:71–75

    Article  CAS  Google Scholar 

  • Jena KK, Kim SM (2010) Current status of brown planthopper (BPH) resistance and genetics. Rice 3:161–171

    Article  Google Scholar 

  • Juliano BO (1985) Criteria and tests for rice grain quality In: Juliano BO (ed) Rice chemistry and technology. American Association of Cereal Chemists, Incorporated, Saint Paul, pp 443–513

  • Kiyosawa S (1972) The inheritance of blast resistance transferred from some indica varieties in rice. Bull Nat Inst Agric Sci Ser D 23:69–96

    Google Scholar 

  • Kumar I, Khush GS (1986) Genetic analysis of different amylose levels in rice. Crop Sci 27:1167–1172

    Article  Google Scholar 

  • Kusaba M, Miyahara K, Iida S, Fukuoka H, Takano T, Sassa H, Nishimura M, Nishio T (2003) Low glutelin content 1: a dominant mutation that suppresses the glutelin multigene family via RNA silencing in rice. Plant Cell 15(6):1455–1467

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Larkin PD, Park WD (2003) Association of waxy gene single nucleotide polymorphisms with starch characteristics in rice (Oryza sativa L.). Mol Breed 12:335–339

    Article  CAS  Google Scholar 

  • Li XB, Yan WG, Agrama H, Hu BL, Jia LM, Jia M, Jackson A, Moldenhauer K, McClung A, Wu DX (2010) Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection. Genetica 138:1221–1230

    Article  CAS  PubMed  Google Scholar 

  • Li XB, Yan WG, Agrama H, Jia LM, Shen XH, Jackson A, Moldenhauer K, Yeater K, McClung A, Wu DX (2011) Mapping QTLs for improving grain yield using the USDA rice mini-core collection. Planta 234:347–361

    Article  CAS  PubMed  Google Scholar 

  • Louis MTB, Robert JH, Jin QS, Russel FR, Daniel LEW (2005) A perfect marker for fragrance genotyping in rice. Mol Breed 16:279–283

    Article  CAS  Google Scholar 

  • Lu FH, Park YJ (2012) An SNP downstream of the OsBEIIb gene is significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.). J Cereal Sci 56:706–712

    Article  CAS  Google Scholar 

  • Lu Y, Xiao P, Shao Y, Zhang G, Thanyasiriwat T, Bao J (2010) Development of new markers to genotype the functional SNPs of SSIIa, a gene responsible for gelatinization temperature of rice starch. J Cereal Sci 52:438–443

    Article  CAS  Google Scholar 

  • Mikami I, Uwatoko N, Ikeda Y, Yamaguchi J, Hirano HY, Suzuki Y, Sano Y (2008) Allelic diversification at the wx locus in landraces of Asian rice. Theor Appl Genet 116(7):979–989

    Article  CAS  PubMed  Google Scholar 

  • Miyahara K, Kusaba M, Sassa E, Iida S, Takano T, Nishio T, Nishio T (1996) Analysis of glutelin gene in rice low glutelin line “LGC-1.” Breed Sci 46(Suppl 1):42

    Google Scholar 

  • Nakamura Y (2002) Towards a better understanding of the metabolic system for amylopectin biosynthesis in plants: rice endosperm as a model tissue. Plant Cell Physiol 43(7):718–725

    Article  CAS  PubMed  Google Scholar 

  • Nakamura Y, Utsumi Y, Sawada T, Aihara S, Utsumi C, Yoshida M, Kitamura S (2010) Characterization of the reactions of starch branching enzymes from rice endosperm. Plant Cell Physiol 51(5):776–794

    Article  CAS  PubMed  Google Scholar 

  • Normile D (2008) Reinventing rice to feed the world. Science 321:330–333

    Article  CAS  PubMed  Google Scholar 

  • Perumalsamy S, Bharani M, Sudha M, Nagarajan P, Arul L, Saraswathi R, Balasubramanian P, Ramalingam J (2010) Functional marker-assisted selection for bacterial leaf blight resistance genes in rice (Oryza sativa L.). Plant Breed 129:400–406

    CAS  Google Scholar 

  • Peter E, Brian R, Graham S (2004) Allele-specific markers within the barley stem rust resistance gene (Rpg 1). Barley Genet Newsl 33:7

    Google Scholar 

  • Qu LQ, Wei XL, Satoh H, Kumamaru T, Ogawa M, Takaiwa F (2002) Inheritance of alleles for glutelin α-2 subunit genes in rice and identification of their corresponding cDNA clone. Theor Appl Genet 105(8):1099–1108

    Article  CAS  PubMed  Google Scholar 

  • Rafalski JA, Tingey SV (1993) Genetic diagnostics in plant breeding: PAPDs, microsatellites and machines. Trends Genet 96:957–963

    Google Scholar 

  • Rahman ML, Jiang WZ, Chu SH, Qiao YL, Ham TH, Woo MO, Lee J, Khanam MS, Chin JH, Jeung JU et al (2009) High resolution mapping of two rice brown planthopper resistance genes, Bph(t) and Bph21(t), originating from Oryza minuta. Theor Appl Genet 119:1237–1246

    Article  PubMed  Google Scholar 

  • Ram T, Laha GS, Gautam SK, Deen R, Madhav MS, Brar DS (2010) Identification of new gene introgressed from Oryza brachyantha with broad-spectrum resistance to bacterial blight of rice in India. Rice Genet Newsl 25:57

    Google Scholar 

  • Ramkumar G, Srinivasarao K, Madhan MK, Sudarshan I, Sivaranjani AKP, Gopaakrishna K, Neeraja CN, Syahariza ZA, Sar S, Hasjim J, Tizzotti MJ, Gilbert RG (2013) The importance of amylose and amylopectin fine structure for starch digestibility in cooked rice grains. Food Chem 136:742–749

    Article  CAS  Google Scholar 

  • Sano Y (1984) Differential regulation of waxy gene expression in rice endosperm. Theor Appl Genet 68:467–473

    Article  CAS  PubMed  Google Scholar 

  • Sano Y, Katsumata M, Amano E (1985) Correlations between the amounts of amylose and Wx protein in rice endosperm. SABRAO J 17:121–127

    Google Scholar 

  • Sharma TR, Chauhan RS, Singh BM, Paul R, Sagar V, Rathore R (2002) RAPD and pathotype analysis of Magnaporthe grisea population from north-western Himalayan region of India. J Phytopathol 150:649–656

    Article  CAS  Google Scholar 

  • Syahariza ZA, Sar S, Hasjim J, Tizzotti MJ, Gilbert RG (2013) The importance of amylose and amylopectin fine structure for starch digestibility in cooked rice grains. Food Chem 136:742–749

    Article  CAS  PubMed  Google Scholar 

  • Teng B, Zeng RZ, Wang YC, Liu ZQ, Zhang ZM, Zhu HT, Ding XH, Li WT, Zhang GQ (2012) Detection of allelic variation at the Wx locus with single-segment substitution lines in rice (Oryza sativa L.). Breed Sci 30:583–595

    Google Scholar 

  • Tester RF, Karkalas J, Qi X (2004) Starch-composition, fine structure and architecture. J Cereal Sci 39:151–165

    Article  CAS  Google Scholar 

  • Umemoto T, Aoki N (2004) Single-nucleotide polymorphisms in rice starch synthase IIa that alter starch gelatinization and starch association of the enzyme. Funct Plant Biol 32:763–768

    Article  Google Scholar 

  • Wanchana S, Toojinda T, Tragoonrung S, Vanavichit A (2003) Duplicated coding sequence in the waxy allele of tropical glutinous rice (Oryza sativa L.). Plant Sci 165:1193–1199

    Article  CAS  Google Scholar 

  • Wang J, Wan X, Li H, Pfeiffer WH, Crouch J, Wan J (2007) Application of identified QTL-marker associations in rice quality improvement through a design-breeding approach. Theor Appl Genet 115:87–100

    Article  PubMed  Google Scholar 

  • Way MJ, Heong KL (1994) The role of biodiversity in the dynamics and management of insect pests of tropical irrigated rice—a review. Bull Entomol Res 84:567–587

    Article  Google Scholar 

  • Yara A, Phi CN, Matsumura M, Yoshimura A, Yasui H (2010) Development of near-isogenic lines for BPH25(t) and BPH26(t), which confer resistance to the brown planthopper, Nilaparvata lugen (Stal.) in indica rice “ADR52.” Breed Sci 60:639–647

    Article  Google Scholar 

  • Zhang G, Cheng Z, Zhang X, Guo X, Su N, Jiang L, Mao L, Wan JM (2011) Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on physic-chemical properties of starch. Genome 54:448–459

    Article  CAS  PubMed  Google Scholar 

  • Zhou L, Chen ZJ, Lang XY, Du B, Liu K, Yang GC, Hu G, Li SH, He GC, You AQ (2013) Development and validation of a PCR-based functional marker system for the brown planthopper resistance gene Bph14 in rice. Breed Sci 63:347–352

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors would like to thank Guizhou University Natural Science Project (2020) 23 and Guizhou University Seed Program (2020) 26 for financial support. We thank the 4th international rice congress for giving us a chance to present orally part of data of this paper in 2014 at Bangkok, Thailand.

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  1. Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China

    Kehu Li, Huanhuan Ren & Yongyi Ge

  2. Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, People’s Republic of China

    Lily Yan Wang

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  1. Kehu Li
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Correspondence to Kehu Li.

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Li, K., Wang, L.Y., Ren, H. et al. Genotyping USDA rice (Oryza spp.) mini-core collection with functional markers for important agronomic traits. Genet Resour Crop Evol 69, 2331–2344 (2022). https://doi.org/10.1007/s10722-022-01375-w

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