Genome-Wide Association Study (GWAS) Reveals an SNP Associated with Waxy Trait and Development of a Functional Marker for Predicting Waxy Maize (<i>Zea mays</i> L. var. ceratina)
Waxy maize (<i>Zea mays</i> L. var. ceratina) is a special type of maize characterized by a sticky texture when cooked, due to high amylopectin content in the endosperm. Waxy maize is popular in China and Southeast Asia for fresh consumption. Breeding strategies have been used to improve...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-09-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/12/10/2289 |
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| author | Vinitchan Ruanjaichon Khin Kyawt Yin Burin Thunnom Kanogporn Khammona Khundej Suriharn Sakunkan Simla Chalong Kerdsri Wanchana Aesomnuk Arweewut Yongsuwan Naraporn Chaomueang Nay Nay Oo Jintana Unartngam Siwaret Arikit Samart Wanchana Theerayut Toojinda |
| author_facet | Vinitchan Ruanjaichon Khin Kyawt Yin Burin Thunnom Kanogporn Khammona Khundej Suriharn Sakunkan Simla Chalong Kerdsri Wanchana Aesomnuk Arweewut Yongsuwan Naraporn Chaomueang Nay Nay Oo Jintana Unartngam Siwaret Arikit Samart Wanchana Theerayut Toojinda |
| author_sort | Vinitchan Ruanjaichon |
| collection | DOAJ |
| description | Waxy maize (<i>Zea mays</i> L. var. ceratina) is a special type of maize characterized by a sticky texture when cooked, due to high amylopectin content in the endosperm. Waxy maize is popular in China and Southeast Asia for fresh consumption. Breeding strategies have been used to improve the quality of waxy maize, including hybrid breeding by crossing super sweet maize and waxy maize. However, the lack of a marker has limited the efficiency of breeding for the waxy trait, especially because the waxy allele is recessive. In this study, we conducted a genome-wide association study (GWAS) in an association panel consisting of 213 inbred lines and recombinant inbred lines (RILs) of field maize and waxy maize to identify loci associated with the waxy kernel phenotype. The genotypic data were 155,768 SNPs derived from the high-density 600 K maize genotyping array for single-nucleotide polymorphisms (SNPs). The GWAS results identified the <i>qWx9</i> locus on chromosome 9 (25.06–25.18 Mb) associated with the trait. Based on the most significantly associated SNP (AX-90613979, −log10(P) = 6.8)), which was located on <i>Wx1,</i> a MassArray marker was developed and validated in a panel of 139 maize lines containing waxy maize and sweet maize with different amylose content. The newly developed marker had a significant association with amylose content (R<sup>2</sup> value of 0.81, <i>p</i> < 0.001) and clearly distinguished between waxy maize and sweet maize lines that had different amylose content. This marker will be useful for maize breeding programs for the waxy trait, as well as for breeding programs for hybrid maize combining the sweetness and waxy traits. The gene-based SNP markers could aid breeders by eliminating the costs and time required to perform lengthy field trials and help to accelerate sweet maize and waxy maize breeding programs. |
| first_indexed | 2024-03-09T20:54:15Z |
| format | Article |
| id | doaj.art-2c30d661577a457c914dcb86b0e1c62d |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-09T20:54:15Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-2c30d661577a457c914dcb86b0e1c62d2023-11-23T22:24:31ZengMDPI AGAgronomy2073-43952022-09-011210228910.3390/agronomy12102289Genome-Wide Association Study (GWAS) Reveals an SNP Associated with Waxy Trait and Development of a Functional Marker for Predicting Waxy Maize (<i>Zea mays</i> L. var. ceratina)Vinitchan Ruanjaichon0Khin Kyawt Yin1Burin Thunnom2Kanogporn Khammona3Khundej Suriharn4Sakunkan Simla5Chalong Kerdsri6Wanchana Aesomnuk7Arweewut Yongsuwan8Naraporn Chaomueang9Nay Nay Oo10Jintana Unartngam11Siwaret Arikit12Samart Wanchana13Theerayut Toojinda14National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandMaster of Science Program in Agricultural Research and Development, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandDepartment of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDepartment of Agricultural Technology, Mahasarakham University, Mahasarakham 44150, ThailandChai Nat Field Crops Research Center, Chai Nat 17000, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandDoctor of Philosophy Program in Agricultural Sciences, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, ThailandDepartment of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, ThailandDepartment of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandWaxy maize (<i>Zea mays</i> L. var. ceratina) is a special type of maize characterized by a sticky texture when cooked, due to high amylopectin content in the endosperm. Waxy maize is popular in China and Southeast Asia for fresh consumption. Breeding strategies have been used to improve the quality of waxy maize, including hybrid breeding by crossing super sweet maize and waxy maize. However, the lack of a marker has limited the efficiency of breeding for the waxy trait, especially because the waxy allele is recessive. In this study, we conducted a genome-wide association study (GWAS) in an association panel consisting of 213 inbred lines and recombinant inbred lines (RILs) of field maize and waxy maize to identify loci associated with the waxy kernel phenotype. The genotypic data were 155,768 SNPs derived from the high-density 600 K maize genotyping array for single-nucleotide polymorphisms (SNPs). The GWAS results identified the <i>qWx9</i> locus on chromosome 9 (25.06–25.18 Mb) associated with the trait. Based on the most significantly associated SNP (AX-90613979, −log10(P) = 6.8)), which was located on <i>Wx1,</i> a MassArray marker was developed and validated in a panel of 139 maize lines containing waxy maize and sweet maize with different amylose content. The newly developed marker had a significant association with amylose content (R<sup>2</sup> value of 0.81, <i>p</i> < 0.001) and clearly distinguished between waxy maize and sweet maize lines that had different amylose content. This marker will be useful for maize breeding programs for the waxy trait, as well as for breeding programs for hybrid maize combining the sweetness and waxy traits. The gene-based SNP markers could aid breeders by eliminating the costs and time required to perform lengthy field trials and help to accelerate sweet maize and waxy maize breeding programs.https://www.mdpi.com/2073-4395/12/10/2289<i>Zea may</i> L.amylopectinamylosewaxyglutinous<i>waxy1</i> |
| spellingShingle | Vinitchan Ruanjaichon Khin Kyawt Yin Burin Thunnom Kanogporn Khammona Khundej Suriharn Sakunkan Simla Chalong Kerdsri Wanchana Aesomnuk Arweewut Yongsuwan Naraporn Chaomueang Nay Nay Oo Jintana Unartngam Siwaret Arikit Samart Wanchana Theerayut Toojinda Genome-Wide Association Study (GWAS) Reveals an SNP Associated with Waxy Trait and Development of a Functional Marker for Predicting Waxy Maize (<i>Zea mays</i> L. var. ceratina) Agronomy <i>Zea may</i> L. amylopectin amylose waxy glutinous <i>waxy1</i> |
| title | Genome-Wide Association Study (GWAS) Reveals an SNP Associated with Waxy Trait and Development of a Functional Marker for Predicting Waxy Maize (<i>Zea mays</i> L. var. ceratina) |
| title_full | Genome-Wide Association Study (GWAS) Reveals an SNP Associated with Waxy Trait and Development of a Functional Marker for Predicting Waxy Maize (<i>Zea mays</i> L. var. ceratina) |
| title_fullStr | Genome-Wide Association Study (GWAS) Reveals an SNP Associated with Waxy Trait and Development of a Functional Marker for Predicting Waxy Maize (<i>Zea mays</i> L. var. ceratina) |
| title_full_unstemmed | Genome-Wide Association Study (GWAS) Reveals an SNP Associated with Waxy Trait and Development of a Functional Marker for Predicting Waxy Maize (<i>Zea mays</i> L. var. ceratina) |
| title_short | Genome-Wide Association Study (GWAS) Reveals an SNP Associated with Waxy Trait and Development of a Functional Marker for Predicting Waxy Maize (<i>Zea mays</i> L. var. ceratina) |
| title_sort | genome wide association study gwas reveals an snp associated with waxy trait and development of a functional marker for predicting waxy maize i zea mays i l var ceratina |
| topic | <i>Zea may</i> L. amylopectin amylose waxy glutinous <i>waxy1</i> |
| url | https://www.mdpi.com/2073-4395/12/10/2289 |
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