SNP discovery in proso millet (Panicum miliaceum L.) using low‐pass genome sequencing
Abstract Domesticated ~10,000 years ago in northern China, Proso millet (Panicum miliaceum L.) is a climate‐resilient and human health‐promoting cereal crop. The genome size of this self‐pollinated allotetraploid is 923 Mb. Proso millet seeds are an important part of the human diet in many countries...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2022-09-01
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| Series: | Plant Direct |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/pld3.447 |
| _version_ | 1797822540434898944 |
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| author | Rituraj Khound Guangchao Sun Ravi V. Mural James C. Schnable Dipak K. Santra |
| author_facet | Rituraj Khound Guangchao Sun Ravi V. Mural James C. Schnable Dipak K. Santra |
| author_sort | Rituraj Khound |
| collection | DOAJ |
| description | Abstract Domesticated ~10,000 years ago in northern China, Proso millet (Panicum miliaceum L.) is a climate‐resilient and human health‐promoting cereal crop. The genome size of this self‐pollinated allotetraploid is 923 Mb. Proso millet seeds are an important part of the human diet in many countries. In the USA, its use is restricted to the birdseed and pet food market. Proso millet is witnessing gradual demand in the global human health and wellness food market owing to its health‐promoting properties such as low glycemic index and gluten‐free. The breeding efforts for developing improved proso millet cultivars are hindered by the dearth of genomic resources available to researchers. The publication of the reference genome and availability of cost‐effective NGS methodologies could lead to the identification of high‐quality genetic variants, which can be incorporated into breeding pipelines. Here, we report the identification of single‐nucleotide polymorphisms (SNPs) by low‐pass (1×) genome sequencing of 85 diverse proso millet accessions from 23 different countries. The 2 × 150 bp Illumina paired‐end reads generated after sequencing were aligned to the proso millet reference genome. The resulting sequence alignment information was used to call SNPs. We obtained 972,863 bi‐allelic SNPs after quality filtering of the raw SNPs. These SNPs were used to assess the population structure and phylogenetic relationships among the accessions. Most of the accessions were found to be highly inbred with heterozygosity ranging between .05 and .20. Principal component analysis (PCA) showed that PC1 (principal component) and PC2 explained 19% of the variability in the population. PCA also clustered all the genotypes into three groups. A neighbor‐joining tree clustered the genotypes into four distinct groups exhibiting diverse representation within the population. The SNPs identified in our study could be used for molecular breeding and genetics research (e.g., genetic and association mapping, and population genetics) in proso millet after proper validation. |
| first_indexed | 2024-03-13T10:10:37Z |
| format | Article |
| id | doaj.art-7c8c9bf2eb9e4a4e8194c3032000b243 |
| institution | Directory Open Access Journal |
| issn | 2475-4455 |
| language | English |
| last_indexed | 2024-03-13T10:10:37Z |
| publishDate | 2022-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | Plant Direct |
| spelling | doaj.art-7c8c9bf2eb9e4a4e8194c3032000b2432023-05-21T21:10:28ZengWileyPlant Direct2475-44552022-09-0169n/an/a10.1002/pld3.447SNP discovery in proso millet (Panicum miliaceum L.) using low‐pass genome sequencingRituraj Khound0Guangchao Sun1Ravi V. Mural2James C. Schnable3Dipak K. Santra4Department of Agronomy and Horticulture University of Nebraska‐Lincoln Lincoln NE USADepartment of Agronomy and Horticulture University of Nebraska‐Lincoln Lincoln NE USADepartment of Agronomy and Horticulture University of Nebraska‐Lincoln Lincoln NE USADepartment of Agronomy and Horticulture University of Nebraska‐Lincoln Lincoln NE USADepartment of Agronomy and Horticulture University of Nebraska‐Lincoln Lincoln NE USAAbstract Domesticated ~10,000 years ago in northern China, Proso millet (Panicum miliaceum L.) is a climate‐resilient and human health‐promoting cereal crop. The genome size of this self‐pollinated allotetraploid is 923 Mb. Proso millet seeds are an important part of the human diet in many countries. In the USA, its use is restricted to the birdseed and pet food market. Proso millet is witnessing gradual demand in the global human health and wellness food market owing to its health‐promoting properties such as low glycemic index and gluten‐free. The breeding efforts for developing improved proso millet cultivars are hindered by the dearth of genomic resources available to researchers. The publication of the reference genome and availability of cost‐effective NGS methodologies could lead to the identification of high‐quality genetic variants, which can be incorporated into breeding pipelines. Here, we report the identification of single‐nucleotide polymorphisms (SNPs) by low‐pass (1×) genome sequencing of 85 diverse proso millet accessions from 23 different countries. The 2 × 150 bp Illumina paired‐end reads generated after sequencing were aligned to the proso millet reference genome. The resulting sequence alignment information was used to call SNPs. We obtained 972,863 bi‐allelic SNPs after quality filtering of the raw SNPs. These SNPs were used to assess the population structure and phylogenetic relationships among the accessions. Most of the accessions were found to be highly inbred with heterozygosity ranging between .05 and .20. Principal component analysis (PCA) showed that PC1 (principal component) and PC2 explained 19% of the variability in the population. PCA also clustered all the genotypes into three groups. A neighbor‐joining tree clustered the genotypes into four distinct groups exhibiting diverse representation within the population. The SNPs identified in our study could be used for molecular breeding and genetics research (e.g., genetic and association mapping, and population genetics) in proso millet after proper validation.https://doi.org/10.1002/pld3.447ancient grainclimate‐resilientpanicoid, C4 photosynthesisphylogenypopulation structure |
| spellingShingle | Rituraj Khound Guangchao Sun Ravi V. Mural James C. Schnable Dipak K. Santra SNP discovery in proso millet (Panicum miliaceum L.) using low‐pass genome sequencing Plant Direct ancient grain climate‐resilient panicoid, C4 photosynthesis phylogeny population structure |
| title | SNP discovery in proso millet (Panicum miliaceum L.) using low‐pass genome sequencing |
| title_full | SNP discovery in proso millet (Panicum miliaceum L.) using low‐pass genome sequencing |
| title_fullStr | SNP discovery in proso millet (Panicum miliaceum L.) using low‐pass genome sequencing |
| title_full_unstemmed | SNP discovery in proso millet (Panicum miliaceum L.) using low‐pass genome sequencing |
| title_short | SNP discovery in proso millet (Panicum miliaceum L.) using low‐pass genome sequencing |
| title_sort | snp discovery in proso millet panicum miliaceum l using low pass genome sequencing |
| topic | ancient grain climate‐resilient panicoid, C4 photosynthesis phylogeny population structure |
| url | https://doi.org/10.1002/pld3.447 |
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