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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (2): 267-279.doi: 10.3724/SP.J.1006.2022.14047

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Phylogeny of wild Setaria species and their utilization in foxtail millet breeding

ZHAO Mei-Cheng1,2(), DIAO Xian-Min2,*()   

  1. 1Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/Hebei Province Key Laboratory for Water-Saving Agriculture, Shijiazhuang 050021, Heibei, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2021-02-02 Accepted:2021-05-17 Online:2022-02-12 Published:2021-05-24
  • Contact: DIAO Xian-Min E-mail:mczhao@sjziam.ac.cn;diaoxianmin@caas.cn
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2019YFD1000700);This study was supported by the National Key Research and Development Program of China(2019YFD1000701);This study was supported by the National Key Research and Development Program of China(2018YFD1000706);This study was supported by the National Key Research and Development Program of China(2018YFD1000700);the China Agricultural Research System(CARS-06-13.5-A4);the National Natural Science Foundation of China(31871634);the Natural Science Foundation of Hebei Province(C2020503004)


Foxtail millet (Setaria italica) was domesticated from the wild ancestor, green foxtail (S. viridis), about ten thousand years ago in China. Foxtail millet belongs to Setaria genus, which includes about 125 species of panicoid grasses worldwide, and 15 species of them in China varied from diploid to octoploid. Currently, six genomes in the Setaria genus have been identified by GISH (genomic in situ hybridization). Molecular phylogenetic analyses show that the Setaria genus is polyphyletic, in line with the characteristic of diversified genomes. Phylogeny of Setaria genus reveal that foxtail millet is most closely related with green foxtail, and then S. fabrei and S. verticillata, and that A genome of S. italica/S. viridis appears to be closer to B genome of S. adhaeran and C genome of S. grisebachii than the other known genomes. For utilization of wild species resources, foxtail millet breeders have successfully introduced the naturally mutated herbicide-resistant genes from green foxtail into cultivars, resulting in the herbicide-resistant foxtail millet variety. Here, we review the recent advances of wild species of foxtail millet in species classification, genome constitution and phylogenetic relationships, and highlight the utility of the wild species resources for breeding and domestication of foxtail millet. We also discuss the potentials of the wild Setaria species in discovery of domestication genes and breeding in foxtail millet in the future.

Key words: foxtail millet, wild species, phylogenetic analysis, breeding

Table 1

Geographical distribution and chromosome number of Setaria species (Modified from Kellogg[19])"

Species name
Chromosome number (2n)
S. adhaerens 亚洲 Asia 18
S. apiculata 澳大利亚 Australia 36
S. barbata 非洲 Africa 54, 56
S. faberi 南美洲 South America 36
S. flavida 澳大利亚 Australia 44, 54
S. geminata 非洲 Africa ND
S. grisebachii 北美洲和南美洲 North and South America 18
S. homonyma 非洲 Africa ND
S. italica 亚洲 Asia 18, 36
S. kagerensis 非洲 Africa 18
S. lachnea 南美洲 South America 36
S. leucopila 美国, 墨西哥, 南美洲 USA, Mexico, and South America 54, 68, 72
S. longiseta 非洲 Africa 36
S. macrostachya 北美洲和南美洲 North and South America 54, 72
S. magna 北美洲和南美洲 North and South America 36
S. nigrirostris 非洲 Africa 18, 36, 54
S. oblongata 阿根廷和玻利维亚 Argentina and Bolivia ND
S. palmifolia 亚洲和非洲 Asia and Africa 54, 36
S. pampeana 阿根廷 Argentina 50
S. pflanzii 南美洲 South America 36
S. plicata 亚洲 Asia ND
S. pumila 非洲和亚洲 Africa and Asia 36, 54
S. restioidea 非洲 Africa ND
S. rosengurtii 南美洲 South America ND
S. scabrifolia 南美洲 South America ND
S. sphacelata 非洲 Africa 18, 36, 54
S. sulcata 北美洲和南美洲 North and South America 18, 32, 36
S. tenacissima 北美洲和南美洲 North and South America 54, 36
S. vaginata 南美洲 South America 18
S. verticillata 欧亚大陆 Eurasia 36, 54
S. viridis 亚洲 Asia 18
S. vulpiseta 北美洲和南美洲 North and South America 36, 54

Table 2

Published genome constitutions of Setaria species"

Species name
Accession number
Chromosome number
Genome constitutions
S. viridis 中国河北 Hebei, China N033 2n = 2x = 18 AA
S. viridis 俄罗斯 Russia 09005 2n = 2x = 18 AA
青9 Qing 9 中国河北 Hebei, China N011 2n = 2x = 18 BB
S. adhaerans 西班牙 Spain 02448 2n = 2x = 18 BB
S. adhaerans 美国夏威夷 Hawaii, USA 25001 2n = 2x = 18 BB
S. grisebachii 墨西哥 Mexico 03001 2n = 2x = 18 CC
S. queenslandica 澳大利亚 Australia PI316342 2n = 4x = 36 AAAA
S. lachnea 澳大利亚 Australia 11001 2n = 4x = 36 CCC’C’
S. verticillata 法国 France 08006 2n = 4x = 36 AABB
S. faberi 俄罗斯 Russia 02005 2n = 4x = 36 AABB
S. glauca 美国 USA 04004 2n = 4x = 36 X (DD)
S. glauca 日本 Japan 04002 2n = 8x = 72 X (DD)
S. plicata 中国昆明 Kunming, China 25001 2n = 4x = 36 X (EE)
S. palmifolia 中国昆明 Kunming, China 26001 2n = 6x = 54 X (EE)
S. arenaria 中国昆明 Kunming, China 27001 2n = 6x = 54 X (FF)

Fig. 1

Phylogenetic tree of Setaria species based on the knotted1 and 5S rDNA gene The capital alphabet following the species name indicates the different copies of each gene in the corresponding species, and six genomes (A-F) are identified and distinguished from each other."

Table 3

Identified naturally mutated herbicide-resistance Setaria species"

Year of the first identification
Active ingredients
Site of action
S. viridis 1988 加拿大(曼尼托巴)
Canada (Manitoba)
大麦 Barley
小麦 Wheat
乙丁烯氟灵 Ethalfluralin
氟乐灵 Trifluralin
Microtubule assembly inhibitors
S. viridis 1991 加拿大(曼尼托巴)
Canada (Manitoba)
大麦 Barley
小麦 Wheat
禾草灵 Diclofop-methyl
拿扑净 Sethoxydim
肟草酮 Tralkoxydim
Acetyl CoA carboxylase
S. viridis 1992 加拿大(曼尼托巴)
Canada (Manitoba)
大麦 Barley
油菜 Canola
禾草灵 Diclofop-methyl
拿扑净 Sethoxydim
肟草酮 Tralkoxydim
氟乐灵 Trifluralin
Microtubule assembly and acetyl CoA carboxylase inhibitor
S. viridis 2001 加拿大(安大略省)
Canada (Ontario)
玉米 Maize
大豆 Soybean
氟酮磺隆 Flucarbazone
咪唑乙烟酸 Imazethapyr
烟嘧磺隆 Nicosulfuron
嘧草硫醚 Pyrithiobac
Acetolactate synthase inhibitor
S. viridis 1982 法国 France 玉米 Maize 阿特拉津 Atrazine 光合作用光系统II抑制剂
Photosystem II inhibitor
S. viridis 1987 西班牙 Spain 玉米 Maize 阿特拉津 Atrazine 光合作用光系统II抑制剂
Photosystem II inhibitor
S. viridis 1989 美国(北达科他州)
USA (North Dakota)
向日葵 Sunflower
小麦 Wheat
氟乐灵 Trifluralin 微管抑制剂
Microtubule assembly inhibitors
S. viridis 1999 美国(威斯康星州)
USA (Wisconsin)
玉米 Maize
大豆 Soybean
甲氧咪草烟 Imazamox 乙酰乳酸合成酶抑制剂
Acetolactate synthase inhibitor
S. verticillata 1992 西班牙 Spain 玉米 Maize 阿特拉津 Atrazine 光合作用光系统II抑制剂
Photosystem II inhibitor
S. faberi 2003 加拿大(安大略省)
Canada (Ontario)
大豆 Soybean 咪唑乙烟酸 Imazethapyr 乙酰乳酸合成酶抑制剂
Acetolactate synthase inhibitor
S. faberi 1987 西班牙 Spain 玉米 Maize 阿特拉津 Atrazine 光合作用光系统II抑制剂
Photosystem II inhibitor
S. faberi 1984 美国(马里兰州)
USA (Maryland)
玉米 Maize 阿特拉津 Atrazine 光合作用光系统II抑制剂
Photosystem II inhibitor
S. faberi 1991 美国(威斯康星州)
USA (Wisconsin)
胡萝卜 Carrot
玉米 Maize
洋葱 Onion
氟禾草灵 Fluazifop-butyl
拿扑净 Sethoxydim
Acetyl CoA carboxylase
S. faberi 1999 美国(威斯康星州)
USA (Wisconsin)
玉米 Maize
大豆 Soybean
咪唑乙烟酸 Imazethapyr
烟嘧磺隆 Nicosulfuron
Acetolactate synthase inhibitor
S. glauca 1997 美国(明尼苏达州)
USA (Minnesota)
大豆 Soybean 咪唑乙烟酸 Imazethapyr 乙酰乳酸合成酶抑制剂
Acetolactate synthase inhibitor
S. glauca 1981 法国 France 玉米 Maize 阿特拉津 Atrazine 光合作用光系统II抑制剂
Photosystem II inhibitor
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