1
|
Liu D, Cui Y, He J, Li S, Li Q, Liang D, Wang J, Shi X, Wang C, Dong K, Liu T, Zhang L, Ren R, Yang T, Feng G, Liu Z. Genetic Diversity and Classification of the Cytoplasm of Chinese Elite Foxtail Millet [ Setaria italica (L.) P. Beauv.] Parental Lines Revealed by Chloroplast Deoxyribonucleic Acid Variation. Front Genet 2019; 10:1198. [PMID: 31824578 PMCID: PMC6882946 DOI: 10.3389/fgene.2019.01198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/29/2019] [Indexed: 12/03/2022] Open
Abstract
Due to the maternal inheritance of cytoplasm, using foxtail millet [Setaria italica (L.) P. Beauv.] male sterile lines with a single cytoplasmic source as the female parent will inevitably lead to a narrow source of cytoplasm in hybrids, which may make them vulnerable to infection by cytoplasm-specific pathogens, ultimately leading to destructive yield losses. To assess cytoplasmic genetic diversity in plants, molecular markers derived from chloroplast DNA (cpDNA) have been used. However, such markers have not yet been applied to foxtail millet. In this study, we designed and screened nine pairs of polymorphic foxtail millet-specific primers based on its completely sequenced cpDNA. Using these primers, we analyzed the genetic diversity and cytoplasmic types of 130 elite foxtail millet parental lines collected in China. Our results revealed that the cytoplasmic genetic diversity of these accessions was low and needs to be increased. The parental lines were divided into four cytoplasmic types according to population structure analysis and a female parent-derivative evolutionary graph, indicating that the cytoplasmic types of elite foxtail millet lines were rather limited. A principal component analysis (PCA) plot was linked with the geographic and ecological distribution of accessions for each cytoplasmic type, as well as their basal maternal parents. Collectively, our results suggest that enriching cytoplasmic sources through the use of accessions from diverse ecological regions and other countries as the female parent may improve foxtail millet breeding programs, and prevent infection by cytoplasm-specific pathogens.
Collapse
Affiliation(s)
- Dan Liu
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yanjiao Cui
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Jihong He
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Suying Li
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Qiang Li
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Dan Liang
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Jianhe Wang
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xiaowei Shi
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Conglei Wang
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Kongjun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Tianpeng Liu
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Lei Zhang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Ruiyu Ren
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Gang Feng
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Zhengli Liu
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| |
Collapse
|
2
|
Muktar MS, Teshome A, Hanson J, Negawo AT, Habte E, Domelevo Entfellner JB, Lee KW, Jones CS. Genotyping by sequencing provides new insights into the diversity of Napier grass (Cenchrus purpureus) and reveals variation in genome-wide LD patterns between collections. Sci Rep 2019; 9:6936. [PMID: 31061417 PMCID: PMC6502793 DOI: 10.1038/s41598-019-43406-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
Napier grass is an important tropical forage-grass and of growing potential as an energy crop. One-hundred-five Napier grass accessions, encompassing two independent collections, were subjected to genotyping by sequencing which generated a set of high-density genome-wide markers together with short sequence reads. The reads, averaging 54 nucleotides, were mapped to the pearl millet genome and the closest genes and annotation information were used to select candidate genes linked to key forage traits. 980 highly polymorphic SNP markers, distributed across the genome, were used to assess population structure and diversity with seven-subgroups identified. A few representative accessions were selected with the objective of distributing subsets of a manageable size for further evaluation. Genome-wide linkage disequilibrium (LD) analyses revealed a fast LD-decay, on average 2.54 kbp, in the combined population with a slower LD-decay in the ILRI collection compared with the EMBRAPA collection, the significance of which is discussed. This initiative generated high-density markers with a good distribution across the genome. The diversity analysis revealed the existence of a substantial amount of variation in the ILRI collection and identified some unique materials from the EMBRAPA collection, demonstrating the potential of the overall population for further genetic and marker-trait-association studies.
Collapse
Affiliation(s)
- Meki S Muktar
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Abel Teshome
- Teagasc
- CELUP Crop Research, Oak Park, Carlow, R93 XE12, Ireland
| | - Jean Hanson
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Alemayehu T Negawo
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Ermias Habte
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | | | - Ki-Won Lee
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Chris S Jones
- Feed and Forage Development, International Livestock Research Institute, Nairobi, Kenya.
| |
Collapse
|
3
|
Kuo SM, Chen YR, Yin SY, Ba QX, Tsai YC, Kuo WHJ, Lin YR. Waxy allele diversification in foxtail millet (Setaria italica) landraces of Taiwan. PLoS One 2018; 13:e0210025. [PMID: 30596758 PMCID: PMC6312202 DOI: 10.1371/journal.pone.0210025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/14/2018] [Indexed: 12/19/2022] Open
Abstract
Foxtail millet (Setaria italica (L.) P. Beauv.), the second most cultivated millet species, is well adapted to diverse environments and remains an important cereal food and forage crop in arid and semiarid regions worldwide. A symbolic crop for indigenous Austronesian peoples, foxtail millet has been cultivated in Taiwan for more than 5,000 years, and landraces reflect diversifying selection for various food applications. A total of 124 accessions collected within Taiwan were assessed for Wx genotypes. Four identified Wx alleles, I, III, IV, and IX were caused by insertion of various transposable elements (TEs) and resulted in endosperm with non-waxy, low amylose content (AC), and waxy, respectively. A total of 16.9%, 4.0%, 49.2%, and 29.8% of accessions were classified as type I, III, IV, and IX, respectively; approximately half of the accessions belonged to the waxy type, indicating that glutinous grains were favored for making traditional food and wine. The TE insertion affected splicing efficiency rather than accuracy, leading to significantly reduced expression of wx in types III, IV, and IX, although their transcripts were the same as wild-type, type I. Consequently, the granule-bound starch synthase I (GBSSI) contents of the three mutated genotypes were relatively low, leading to waxy or low AC endosperm, and the Wx genotypes could explain 78% of variance in AC. The geographic distribution of Wx genotypes are associated with culinary preferences and migration routes of Taiwanese indigenous peoples-in particular, the genotype of landraces collected from Orchid Island was distinct from those from Taiwan Island. This information on the major gene regulating starch biosynthesis in foxtail millet endosperm can be applied to breeding programs for grain quality, and contributes to knowledge of Austronesian cultures.
Collapse
Affiliation(s)
- Shu-meng Kuo
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yu-ru Chen
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Song-yu Yin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Qing-xiong Ba
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yuan-ching Tsai
- Department of Agronomy, National Chiayi University, Chiayi, Taiwan
| | - Warren H. J. Kuo
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yann-rong Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| |
Collapse
|