Genetic Diversity and Geographic Distribution of North American Setaria viridis Populations

Huang, Pu; Feldman, Maximillian

doi:10.1007/978-3-319-45105-3_3

Cited by 6 publications

(6 citation statements)

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“…The population structure is important for explaining the heterogeneity of genetic architecture and is mainly affected by spatial and gene exchange isolation [ 50 ]. Based on 9642 DArT markers, population structure and patterns of relationship of 439 inbred lines was investigated based on different complementary approaches that clearly revealed the existence of genetically distinct groups in the present panel of inbred lines (Figs.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa

et al. 2021

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Background Assessment and effective utilization of genetic diversity in breeding programs is crucial for sustainable genetic improvement and rapid adaptation to changing breeding objectives. During the past two decades, the commercialization of the early and extra-early maturing cultivars has contributed to rapid expansion of maize into different agro-ecologies of sub-Saharan Africa (SSA) where maize has become an important component of the agricultural economy and played a vital role in food and nutritional security. The present study aimed at understanding the population structure and genetic variability among 439 early and extra-early maize inbred lines developed from three narrow-based and twenty-seven broad-based populations by the International Iinstitute of Tropical Agriculture Maize Improvement Program (IITA-MIP). These inbreds were genotyped using 9642 DArTseq-based single nucleotide polymorphism (SNP) markers distributed uniformly throughout the maize genome. Results About 40.8% SNP markers were found highly informative and exhibited polymorphic information content (PIC) greater than 0.25. The minor allele frequency and PIC ranged from 0.015 to 0.500 and 0.029 to 0.375, respectively. The STRUCTURE, neighbour-joining phylogenetic tree and principal coordinate analysis (PCoA) grouped the inbred lines into four major classes generally consistent with the selection history, ancestry and kernel colour of the inbreds but indicated a complex pattern of the genetic structure. The pattern of grouping of the lines based on the STRUCTURE analysis was in concordance with the results of the PCoA and suggested greater number of sub-populations (K = 10). Generally, the classification of the inbred lines into heterotic groups based on SNP markers was reasonably reliable and in agreement with defined heterotic groups of previously identified testers based on combining ability studies. Conclusions Complete understanding of potential heterotic groups would be difficult to portray by depending solely on molecular markers. Therefore, planned crosses involving representative testers from opposing heterotic groups would be required to refine the existing heterotic groups. It is anticipated that the present set of inbreds could contribute new beneficial alleles for population improvement, development of hybrids and lines with potential to strengthen future breeding programs. Results of this study would help breeders in formulating breeding strategies for genetic enhancement and sustainable maize production in SSA.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa

et al. 2021

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“…Crop wild relatives are often poorly represented in germplasm collections (Hunt, Badakshi, Howe, Jones, & Heslop‐Harrison, 2014 ). Thanks to recent collecting efforts, representative collections of green foxtail now exist for both North America (Huang & Feldman, 2017 ) and China (Jia et al., 2013 ). Future collection efforts spanning Eurasia would be worthwhile to understand the cross‐continental population genomics of this global weed and explore genetic introgression of green foxtail into foxtail millet.…”

Section: Discussionmentioning

confidence: 99%

Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping‐by‐sequencing

et al. 2021

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Foxtail millet [Setaria italica (L.) P. Beauv.] is the second most important millet species globally and is adapted to cultivation in diverse environments. Like its wild progenitor, green foxtail [S. viridis (L.) P. Beauv.], it is a model species for C4 photosynthetic pathways and stress tolerance genes in related bioenergy crops. We addressed questions regarding the evolution and spread of foxtail millet through a population genomic study of landraces from across its cultivated range in Europe, Asia, and Africa. We sought to determine population genomic structure and the relationship of domesticated lineages relative to green foxtail. Further, we aimed to identify genes involved in environmental stress tolerance that have undergone differential selection between geographical and genetic groups. Foxtail millet landrace accessions (n = 328) and green foxtail accessions (n = 12) were sequenced by genotyping‐by‐sequencing (GBS). After filtering, 5,677 single nucleotide polymorphisms (SNPs) were retained for the combined foxtail millet−green foxtail dataset and 5,020 for the foxtail millet dataset. We extended geographic coverage of green foxtail by including previously published GBS sequence tags, yielding a 4,515‐SNP dataset for phylogenetic reconstruction. All foxtail millet samples were monophyletic relative to green foxtail, suggesting a single origin of foxtail millet, although no group of foxtail millet was clearly the most ancestral. Four genetic clusters were found within foxtail millet, each with a distinctive geographical distribution. These results, together with archaeobotanical evidence, suggest plausible routes of spread of foxtail millet. Selection scans identified nine candidate genes potentially involved in environmental adaptations, particularly to novel climates encountered, as domesticated foxtail millet spread to new altitudes and latitudes.

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“…Therefore, studies on the full diversity of the crop, foxtail millet, are limited to Chinese researchers at this time. Fortunately, studies on North American green foxtail wild diversity reveal that much of the species diversity is found there ( Huang et al, 2014 ; Huang and Feldman, 2017 ; Schroder et al, 2017 ), a finding that will be important for future researchers. Another important aspect of the Setaria system is the promise of easy transformability, although there is as yet no published reports of transformation being used to confirm gene function.…”

Section: Discussionmentioning

confidence: 99%

“…Green foxtail accessions in China show a strong relationship to Chinese foxtail millet accessions, indicative of continued gene flow after domestication. The Chinese green foxtail accessions are distinct from populations in North America, some of which apparently arrived there prior to European settlement ( Huang et al, 2014 ; Huang and Feldman, 2017 ; Schroder et al, 2017 ).…”

Section: The Domestication Of Foxtail Milletmentioning

confidence: 99%

“…Although several QTLs have been successfully identified from agronomically important traits, as reviewed above, the fine mapping of candidate genes is still challenging, mostly due to the lack of high density marker maps and high-quality reference genomes ( Huang et al, 2016 ). However, the application of next generation sequencing in diverse collections of foxtail millet cultivars ( Jia et al, 2013b ) and wild green foxtail accessions ( Huang and Feldman, 2017 ) are enabling the discovery of genomic variations on a large-scale. 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 ).…”

Section: Perspectives For Future Breedingmentioning

confidence: 99%

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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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Genetic Diversity and Geographic Distribution of North American Setaria viridis Populations

Cited by 6 publications

References 40 publications

Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa

Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa

Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping‐by‐sequencing

Domestication and Improvement in the Model C4 Grass, Setaria

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