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SNP discovery in proso millet ( Panicum miliaceum L.) using low‐pass genome sequencing

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...

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Autores principales: Khound, Rituraj, Sun, Guangchao, Mural, Ravi V., Schnable, James C., Santra, Dipak K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9470529/
https://www.ncbi.nlm.nih.gov/pubmed/36176305
http://dx.doi.org/10.1002/pld3.447
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author Khound, Rituraj
Sun, Guangchao
Mural, Ravi V.
Schnable, James C.
Santra, Dipak K.
author_facet Khound, Rituraj
Sun, Guangchao
Mural, Ravi V.
Schnable, James C.
Santra, Dipak K.
author_sort Khound, Rituraj
collection PubMed
description 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.
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spelling pubmed-94705292022-09-28 SNP discovery in proso millet ( Panicum miliaceum L.) using low‐pass genome sequencing Khound, Rituraj Sun, Guangchao Mural, Ravi V. Schnable, James C. Santra, Dipak K. Plant Direct Original Research 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. John Wiley and Sons Inc. 2022-09-13 /pmc/articles/PMC9470529/ /pubmed/36176305 http://dx.doi.org/10.1002/pld3.447 Text en © 2022 The Authors. Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Khound, Rituraj
Sun, Guangchao
Mural, Ravi V.
Schnable, James C.
Santra, Dipak K.
SNP discovery in proso millet ( Panicum miliaceum L.) using low‐pass genome sequencing
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 Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9470529/
https://www.ncbi.nlm.nih.gov/pubmed/36176305
http://dx.doi.org/10.1002/pld3.447
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