Mapping QTLs for morpho-agronomic traits in proso millet (Panicum miliaceum L.)

Rajput, Santosh G.; Santra, Dipak K.; Schnable, James C.

doi:10.1007/s11032-016-0460-4

Cited by 58 publications

(38 citation statements)

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“…Rajput et al (2016) constructed the first genetic linkage map of proso millet using SNP markers discovered through genotype-by-sequencing (GBS), an application of next-generation sequencing (NGS) protocols (He et al, 2014). Initially, 69,981 SNPs with a minor allele frequency of >0.05 were identified from raw DNA sequence reads.…”

Section: Genetics and Genomics Of Proso Milletmentioning

confidence: 99%

“…Since this is the first genetic map for proso millet, each linkage group was considered a chromosome as the haploid genome of proso millet has 18 chromosomes. Using these SNP markers, Rajput et al (2016) mapped 18 quantitative trait loci (QTL) for eight traits, namely lodging, heading date, plant height, peduncle length, panicle length, grain shattering, 100 grain weight, and grains per panicle. These QTLs accounted for medium to high phenotypic variance (13–35%).…”

Section: Genetics and Genomics Of Proso Milletmentioning

confidence: 99%

“…In the U.S., there are 15 cultivars of proso millet available to growers. Nine of these cultivars were selections from adapted landraces, and six were developed through hybridization followed by traditional breeding (Rajput et al, 2016). The variety ‘Dawn’ was the first of the modern proso varieties, and is the parent of most of the cultivars released in Nebraska (Lyon et al, 2008a).…”

Section: Genetics and Genomics Of Proso Milletmentioning

confidence: 99%

“…Previously, inadequate molecular markers combined with the challenges of a tetraploid genome such as inconsistent meiotic processes, allelic and non-allelic combinations, and poor correlation between genotype and phenotype (Saha et al, 2016) have made it difficult to conduct genetic and genomic studies in proso millet. However, with the discovery of SNPs by GBS (Rajput et al, 2016) and the identification of differentially expressed genes and thousands of SSR and SNP loci by transcriptome analysis (Yue et al, 2016a,b), a considerable number of molecular markers are currently available for genomic research in proso millet.…”

Section: Genetics and Genomics Of Proso Milletmentioning

confidence: 99%

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Proso Millet (Panicum miliaceum L.) and Its Potential for Cultivation in the Pacific Northwest, U.S.: A Review

et al. 2017

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Proso millet (Panicum miliaceum L.) is a warm season grass with a growing season of 60–100 days. It is a highly nutritious cereal grain used for human consumption, bird seed, and/or ethanol production. Unique characteristics, such as drought and heat tolerance, make proso millet a promising alternative cash crop for the Pacific Northwest (PNW) region of the United States. Development of proso millet varieties adapted to dryland farming regions of the PNW could give growers a much-needed option for diversifying their predominantly wheat-based cropping systems. In this review, the agronomic characteristics of proso millet are discussed, with emphasis on growth habits and environmental requirements, place in prevailing crop rotations in the PNW, and nutritional and health benefits. The genetics of proso millet and the genomic resources available for breeding adapted varieties are also discussed. Last, challenges and opportunities of proso millet cultivation in the PNW are explored, including the potential for entering novel and regional markets.

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Section: Genetics and Genomics Of Proso Milletmentioning

confidence: 99%

Section: Genetics and Genomics Of Proso Milletmentioning

confidence: 99%

Section: Genetics and Genomics Of Proso Milletmentioning

confidence: 99%

Section: Genetics and Genomics Of Proso Milletmentioning

confidence: 99%

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Proso Millet (Panicum miliaceum L.) and Its Potential for Cultivation in the Pacific Northwest, U.S.: A Review

et al. 2017

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“…Although many quantitative trait loci (QTLs) have been identified for various agronomic traits such as plant height, flowering time, lodging, and drought tolerance (Mauro-Herrera et al, 2013; Parvathaneni et al, 2013; Sato et al, 2013; Babu et al, 2014; Qie et al, 2014; Mauro-Herrera and Doust, 2016; Rajput et al, 2016), the QTL intervals are often large (>1 Mb) and difficult to fine map. A partial solution is to generate high density linkage maps using technologies like genotyping by sequencing (Moumouni et al, 2015; Fang et al, 2016; Rajput et al, 2016), but the ultimate solution is to build high-quality reference genomes. To date, foxtail millet remains the only millet that has a chromosomal scale genome assembly (Bennetzen et al, 2012; Zhang et al, 2012), while Eragrostis tef has a draft genome (Cannarozzi et al, 2014), and the genome sequencing of finger millet and pearl millets are still ongoing ( Table 1 ).…”

Section: Advances Of Forward Genetics In Setaria and Other Milletsmentioning

confidence: 99%

Setaria viridis as a Model System to Advance Millet Genetics and Genomics

et al. 2016

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Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops.

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

et al. 2022

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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 costeffective 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 (1Â) genome sequencing of 85 diverse proso millet accessions from 23 different countries. The 2 Â 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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Mapping QTLs for morpho-agronomic traits in proso millet (Panicum miliaceum L.)

Cited by 58 publications

References 57 publications

Proso Millet (Panicum miliaceum L.) and Its Potential for Cultivation in the Pacific Northwest, U.S.: A Review

Proso Millet (Panicum miliaceum L.) and Its Potential for Cultivation in the Pacific Northwest, U.S.: A Review

Setaria viridis as a Model System to Advance Millet Genetics and Genomics

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

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