Genetic analysis of NEKODE1 gene involved in panicle branching of foxtail millet, Setaria italica (L.) P. Beauv., and mapping by using QTL-seq

Masumoto, Hisato; Takagi, Hiroki; Mukainari, Yohei; Terauchi, Ryohei; Fukunaga, Kenji

doi:10.1007/s11032-016-0481-z

Cited by 16 publications

(7 citation statements)

References 32 publications

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“…High-throughput genotyping by sequencing is an option for efficient marker-assisted breeding [ 45 ]. Currently, there are many new methods using NGS for identifying genes or QTLs, including GWAS [ 46 ], QTL-seq [ 47 ], MutMap [ 48 ], RAD-seq [ 35 ], and SLAF-seq [ 49 ], and some have been applied to foxtail millet [ 15 , 30 , 31 ]. However, the utility of RAD-seq has yet not been reported.…”

Section: Resultsmentioning

confidence: 99%

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A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq

Wang

et al. 2017

PLoS ONE

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Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits. In this study, a high-throughput and cost-effective RAD-seq approach was employed to generate a high-density genetic map for foxtail millet. A total of 2,668,587 SNP loci were detected according to the reference genome sequence; meanwhile, 9,968 SNP markers were used to genotype 124 F2 progenies derived from the cross between Hongmiaozhangu and Changnong35; a high-density genetic map spanning 1648.8 cM, with an average distance of 0.17 cM between adjacent markers was constructed; 11 major QTLs for eight agronomic traits were identified; five co-dominant DNA markers were developed. These findings will be of value for the identification of candidate genes and marker-assisted selection in foxtail millet.

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Section: Resultsmentioning

confidence: 99%

“…Bai et al [ 15 ] re-sequenced the foxtail millet landrace ‘Shi-Li-Xiang’ (SLX) and finely mapped a waxy gene using newly developed DNA markers. Masumot et al [ 31 ] carried out QTL-seq and rapidly mapped the NEKODE1 gene responsible for tip-branched panicle.…”

Section: Introductionmentioning

confidence: 99%

A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq

Wang

et al. 2017

PLoS ONE

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“…Meanwhile, the use of bulked segregant analysis (BSA) to quickly analyze mutant collections generated by chemical mutagenesis ( Jiang et al, 2017 ) is accelerating Setaria gene discovery ( Xue et al, 2016 ; Fan et al, 2017 ; Huang et al, 2017 ). New genes contributing to leaf color ( Li et al, 2016 ), height, and inflorescence architecture ( Masumoto et al, 2016 ; Huang et al, 2017 ; Xiang et al, 2017 ; Yang et al, 2018 ) have been successfully identified with this approach, substantially advancing our understanding of important traits.…”

Section: Perspectives For Future Breedingmentioning

confidence: 99%

Domestication and Improvement in the Model C4 Grass, Setaria

Mauro-Herrera

Doust

2018

Front. Plant Sci.

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Setaria viridis (green foxtail) and its domesticated relative S. italica (foxtail millet) are diploid C4 panicoid grasses that are being developed as model systems for studying grass genomics, genetics, development, and evolution. According to archeological evidence, foxtail millet was domesticated from green foxtail approximately 9,000 to 6,000 YBP in China. Under long-term human selection, domesticated foxtail millet developed many traits adapted to human cultivation and agricultural production. In comparison with its wild ancestor, foxtail millet has fewer vegetative branches, reduced grain shattering, delayed flowering time and less photoperiod sensitivity. Foxtail millet is the only present-day crop in the genus Setaria, although archeological records suggest that other species were domesticated and later abandoned in the last 10,000 years. We present an overview of domestication in foxtail millet, by reviewing recent studies on the genetic regulation of several domesticated traits in foxtail millet and discuss how the foxtail millet and green foxtail system could be further developed to both better understand its domestication history, and to provide more tools for future breeding efforts.

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“…Using this method, Li et al (2016) mapped a yellow–green leaf mutation in foxtail millet to a chlorophyll biosynthesis related gene SiYGL1 . Masumoto et al (2016) mapped a branching panicle mutation, a yield related trait in foxtail millet, to a candidate gene NEKODE1 . In chemically induced mutants of S. viridis , BSA can be expected to define causative mutations to a one to few gene interval within two generations (<7 months).…”

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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Genetic analysis of NEKODE1 gene involved in panicle branching of foxtail millet, Setaria italica (L.) P. Beauv., and mapping by using QTL-seq

Abstract: We carried out genetic analysis and map

Cited by 16 publications

References 32 publications

A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq

A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq

Domestication and Improvement in the Model C4 Grass, Setaria

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

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