Development and validation of breeder-friendly functional markers of sugary1 gene encoding starch-debranching enzyme affecting kernel sweetness in maize (Zea mays)
Rashmi Chhabra A , Firoz Hossain
A B , Vignesh Muthusamy A , Aanchal Baveja A , Brijesh K. Mehta A and Rajkumar U. Zunjare A
+ Author Affiliations
- Author Affiliations
A Maize Genetics Unit, Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110 012, India.
B Corresponding author. Email: fh_gpb@yahoo.com
Crop and Pasture Science 70(10) 868-875 https://doi.org/10.1071/CP19298
Submitted: 22 July 2019 Accepted: 29 August 2019 Published: 29 October 2019
Abstract
The sweet corn variety of maize (Zea mays L.) has become popular worldwide. The recessive allele of sugary1 (su1) encoding starch de-branching enzyme has been much used for sweet corn cultivar development. Here, we aimed to develop su1-based functional marker(s) by using six diverse inbred lines of sugary type and five inbred lines of wild type, and using 27 overlapping primers. In total, 12 indels (insertion and deletion) and 96 SNPs (single nucleotide polymorphisms) were identified that clearly differentiated the dominant and recessive allele of su1. Among these, a 36-bp indel (at position 1247) in the promoter region included a TATA-box, and a 6-bp indel (at position 6456) in intron-10 was predicted to have SRp40 exon-splicing enhancer. Nucleotide substitution in exon-2 at position 2703 (SNP-2703) was involved in C to G mutation leading to conversion of phenylalanine to leucine. The 6-bp and 36-bp indels and SNP-2703 were used to develop breeder-friendly codominant markers: SuDel6-FR, SuDel36-FR and SNP2703-CG-85/89. All three markers were validated in five F2 populations, and SuDel36-FR and SNP2703-CG-85/89 were validated in a set of 230 diverse inbreds having both mutant and wild-type alleles of Su1. This is the first report of development and validation of universal functional markers for su1. These markers (SuDel36-FR and SNP2703-CG-85/89) assume great significance in marker-assisted breeding program.
Additional keywords: accelerated breeding, favourable allele, genomics-assisted breeding, gene-based marker, isoamylase 1.
References
Betts MJ, Russell RB (2003) Amino acid properties and consequences of substitutions. In ‘Bioinformatics for geneticists’. Gray, I.C.’ (Eds IC Gray, MR Barnes) (Wiley Publishing: Hoboken, NJ, USA). http://dx.doi.org/10.1002/0470867302.ch14Chhabra R, Hossain F, Muthusamy V, Baveja A, Mehta B, Zunjare RU (2019) Mapping and validation of Anthocyanin1 pigmentation gene for its effectiveness in early selection of shrunken2 gene governing kernel sweetness in maize. Journal of Cereal Science 89, 258–265.
| Mapping and validation of Anthocyanin1 pigmentation gene for its effectiveness in early selection of shrunken2 gene governing kernel sweetness in maize.Crossref | GoogleScholarGoogle Scholar |
Coulombe-Huntington J, Lam KC, Dias C, Majewski J (2009) Fine-scale variation and genetic determinants of alternative splicing across individuals. PLOS Genetics 5, e1000766
| Fine-scale variation and genetic determinants of alternative splicing across individuals.Crossref | GoogleScholarGoogle Scholar | 20011102PubMed |
Dellaporta SL, Wood J, Hicks JB (1985) Maize DNA miniprep. In ‘Plant molecular biology’. (Eds J Malberg, Messing, I Sussex) p. 363. (Cold Spring Harbor Laboratory: Cold Spring Harbor, NY, USA)
Dinges JR, Colleoni C, Myers AM, James MG (2001) Molecular structure of three mutations at the maizesugary1 locus and their allele-specific phenotypic effects. Plant Physiology 125, 1406–1418.
| Molecular structure of three mutations at the maizesugary1 locus and their allele-specific phenotypic effects.Crossref | GoogleScholarGoogle Scholar | 11244120PubMed |
FAOSTAT (2017) FAO, Rome. Available at: www.faostat.org (accessed 22 October 2019).
Feng ZL, Liu J, Fu FL, Li WC (2008) Molecular mechanism of sweet and waxy in maize. International Journal of Plant Breeding and Genetics 2, 93–100.
| Molecular mechanism of sweet and waxy in maize.Crossref | GoogleScholarGoogle Scholar |
Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annual Review of Plant Biology 54, 357–374.
| Structure of linkage disequilibrium in plants.Crossref | GoogleScholarGoogle Scholar | 14502995PubMed |
Gaudet M, Fara AG, Beritognolo I, Sabatti M (2009) Allele-specific PCR in SNP genotyping. Methods in Molecular Biology 578, 415–424.
| Allele-specific PCR in SNP genotyping.Crossref | GoogleScholarGoogle Scholar | 19768609PubMed |
Greenblatt J (1991) Roles of TFIID in transcriptional initiation by RNA polymerase II. Cell 66, 1067–1070.
| Roles of TFIID in transcriptional initiation by RNA polymerase II.Crossref | GoogleScholarGoogle Scholar | 1913802PubMed |
Gupta HS, Vignesh M, Hossain F, Nepolean T (2013) Enrichment of nutritional qualities in maize through marker-assisted selection. In ‘National Seminar on Genomics for Crop Improvement.’ IBAB, Bangalore. (Ed. PK Gupta) pp. 69–70.
Hannah LC, Futch B, Bing J, Shaw JR, Boehlein S, Stewart JD, Beiriger R, Georgelis N, Greene T (2012) A shrunken-2 transgene increases maize yield by acting in maternal tissues to increase the frequency of seed development. The Plant Cell 24, 2352–2363.
| A shrunken-2 transgene increases maize yield by acting in maternal tissues to increase the frequency of seed development.Crossref | GoogleScholarGoogle Scholar | 22751213PubMed |
Hossain F, Nepolean T, Vishwakarma AK, Panday N, Prasanna BM, Gupta HS (2013) Mapping and validation of microsatellite markers linked to sugary1 and shrunken2 genes in maize. Journal of Plant Biochemistry and Biotechnology.
| Mapping and validation of microsatellite markers linked to sugary1 and shrunken2 genes in maize.Crossref | GoogleScholarGoogle Scholar |
Hossain F, Muthusamy V, Pandey N, Vishwakarma AK, Baveja A, Zunjare R, Thirunavukkarasu N, Saha S, Manjaiah KM, Prasanna BM, Gupta HS (2018) Marker-assisted introgression of opaque2 allele for rapid conversion of elite hybrids into quality protein maize. Journal of Genetics 97, 287–298.
| Marker-assisted introgression of opaque2 allele for rapid conversion of elite hybrids into quality protein maize.Crossref | GoogleScholarGoogle Scholar | 29666347PubMed |
James MG, Robertson DS, Myers AM (1995) Characterization of the maize gene sugary1, a determinant of starch composition in kernels. The Plant Cell 7, 417–429.
Lertrat K, Pulam T (2007) Breeding for increased sweetness in sweet corn. International Journal of Plant Breeding 1, 27–30.
Liu J, Huang S, Sun M (2012) An improved allele-specific PCR primer design method for SNP marker analysis and its application. Plant Methods 8, 34
| An improved allele-specific PCR primer design method for SNP marker analysis and its application.Crossref | GoogleScholarGoogle Scholar | 22920499PubMed |
Mehta B, Hossain F, Muthusamy V, Baveja A, Zunjare R, Jha SK, Gupta HS (2017) Microsatellite-based genetic diversity analyses of sugary1-, shrunken2- and double mutant- sweet corn inbreds for their utilization in breeding programme. Physiology and Molecular Biology of Plants 23, 411–420.
| Microsatellite-based genetic diversity analyses of sugary1-, shrunken2- and double mutant- sweet corn inbreds for their utilization in breeding programme.Crossref | GoogleScholarGoogle Scholar | 28461728PubMed |
Muthusamy V, Hossain F, Nepolean T, Choudhary M, Saha S, Bhat JS, Prasanna BM, Gupta HS (2014) Development of β-carotene rich maize hybrids through marker-assisted introgression of β-carotene hydroxylase allele. PLoS One 9, e0122130
| Development of β-carotene rich maize hybrids through marker-assisted introgression of β-carotene hydroxylase allele.Crossref | GoogleScholarGoogle Scholar | 25486271PubMed |
Neuffer MG, Coe EH, Wessler SR (1997) ‘Mutants of maize.’ (Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, USA)
Saghai-Maroof MA, Soliman KM, Jorgenson R, Allard RW (1984) Ribosomal DNA space length polymorphisms in barley: Mendelian inheritance, chromosomal locations and population dynamics. Proceedings of the National Academy of Sciences of the United States of America 81, 8014–8018.
| Ribosomal DNA space length polymorphisms in barley: Mendelian inheritance, chromosomal locations and population dynamics.Crossref | GoogleScholarGoogle Scholar | 6096873PubMed |
Sarika K, Hossain F, Muthusamy V, Zunjare RU, Baveja A, Goswami R, Bhat JS, Saha S, Gupta HS (2018) Marker-assisted pyramiding of opaque2 and novel opaque16 genes for further enrichment of lysine and tryptophan in sub-tropical maize. Plant Science 272, 142–152.
| Marker-assisted pyramiding of opaque2 and novel opaque16 genes for further enrichment of lysine and tryptophan in sub-tropical maize.Crossref | GoogleScholarGoogle Scholar | 29807585PubMed |
Shen R, Fan JB, Campbell D, Chang W, Chen J, Doucet D, Yeakley J, Bibikova M, Wickham GE, McBride C, Steemers F, Garcia F, Kermani BG, Gunderson K, Oliphant A (2005) High-throughput SNP genotyping on universal bead arrays. Mutation Research 573, 70–82.
| High-throughput SNP genotyping on universal bead arrays.Crossref | GoogleScholarGoogle Scholar | 15829238PubMed |
Shin JH, Kwon SJ, Lee JK, Min HK, Kim NS (2006) Genetic diversity of maize kernel starch-synthesis genes with SNAPs. Genome 49, 1287–1296.
| Genetic diversity of maize kernel starch-synthesis genes with SNAPs.Crossref | GoogleScholarGoogle Scholar | 17213911PubMed |
Thiel T, Kota R, Grosse I, Stein N, Graner A (2004) SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Research 32, e5
| SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development.Crossref | GoogleScholarGoogle Scholar | 14704362PubMed |
Tracy WF, Whitt SR, Buckler ES (2006) Recurrent mutation and genome evolution: example of Sugary1 and the origin of sweet maize. Crop Science 46, S49–S54.
| Recurrent mutation and genome evolution: example of Sugary1 and the origin of sweet maize.Crossref | GoogleScholarGoogle Scholar |
Wilson LM, Whitt SR, Ibáñez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of maize kernel composition and starch production by candidate gene association. The Plant Cell 16, 2719–2733.
| Dissection of maize kernel composition and starch production by candidate gene association.Crossref | GoogleScholarGoogle Scholar | 15377761PubMed |
Wu JY, Maniatis T (1993) Specific interaction s between proteins implicated in splice site selection and regulated alternative splicing. Cell 75, 1061–1070.
| Specific interaction s between proteins implicated in splice site selection and regulated alternative splicing.Crossref | GoogleScholarGoogle Scholar | 8261509PubMed |
Wu Y, Zhang Y, Zhang J (2005) Distribution of exonic splicing enhancer elements in human genes. Genomics 86, 329–336.
| Distribution of exonic splicing enhancer elements in human genes.Crossref | GoogleScholarGoogle Scholar | 16005179PubMed |
Zahler AM, Lane WS, Stolk JA, Roth MB (1992) SR proteins: a conserved family of pre-mRNA splicing factors. Genes & Development 6, 837–847.
| SR proteins: a conserved family of pre-mRNA splicing factors.Crossref | GoogleScholarGoogle Scholar |
Zunjare RU, Hossain F, Muthusamy M, Baveja A, Chauhan HS, Bhat JS, Saha S, Gupta HS (2018) Development of multi-nutrient rich maize hybrids through marker-assisted stacking of opaque2 (o2), β-carotene hydroxylase (crtRB1) and lycopene-ϵ-cyclase (lcyE) genes. Frontiers in Plant Science.
| Development of multi-nutrient rich maize hybrids through marker-assisted stacking of opaque2 (o2), β-carotene hydroxylase (crtRB1) and lycopene-ϵ-cyclase (lcyE) genes.Crossref | GoogleScholarGoogle Scholar | 29515602PubMed |
