1
|
Fukunaga K, Abe A, Ito K, Oikawa K, Tsuji M, Kawase M. Latitudinal adaptation and dispersal pathway suggested by geographical distribution of transposable elements inserted in the SiPRR37 gene in foxtail millet. Genes Genet Syst 2024:24-00023. [PMID: 38797684 DOI: 10.1266/ggs.24-00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024] Open
Abstract
We investigated the variation and geographical distribution of the Pseudo-regulator response 37 (Setaria italica PRR37= SiPRR37) gene involved in heading time (photoperiodism) in foxtail millet. An allele of the SiPRR37 gene, in which an approximately 4.9-kb transposable element (designated as TE1 in this article) is inserted (a loss-of-function or reduction-of-function type), is distributed sporadically in East Asia and broadly in Southeast Asia and South Asia, which implies that this gene is important in latitudinal adaptation. In addition, we found a new allele of SiPRR37 with an insertion of a 360-bp TE (designated as TE2) at this locus and investigated the geographical distribution of this new type. This SiPRR37 allele with TE2 is distributed in Japan, Korea, Nepal, Iran, and Turkey. Both TE1 and TE2 are useful markers for tracing foxtail millet dispersal pathways in Asia.
Collapse
Affiliation(s)
- Kenji Fukunaga
- Faculty of Bioresource Sciences, Prefectural University of Hiroshima
| | | | | | | | - Masaya Tsuji
- Graduate School of Comprehensive Scientific Research, Graduate School of Prefectural University of Hiroshima
| | - Makoto Kawase
- Faculty of Agriculture, Tokyo University of Agriculture
| |
Collapse
|
2
|
Fukunaga K, Kawase M. Crop Evolution of Foxtail Millet. PLANTS (BASEL, SWITZERLAND) 2024; 13:218. [PMID: 38256771 PMCID: PMC10819197 DOI: 10.3390/plants13020218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024]
Abstract
Studies on the domestication, genetic differentiation, and crop evolution of foxtail millet are reviewed in this paper. Several genetic studies were carried out to elucidate the genetic relationships among foxtail millet accessions originating mainly from Eurasia based on intraspecific hybrid pollen semi-sterility, isozymes, DNA markers, and single-nucleotide polymorphisms. Most studies suggest that China is the center of diversity of foxtail millet, and landraces were categorized into geographical groups. These results indicate that this millet was domesticated in China and spread over Eurasia, but independent origin in other regions cannot be ruled out. Furthermore, the evolution of genes was reviewed (i.e., the Waxy gene conferring amylose content in the endosperm, the Si7PPO gene controlling polyphenol oxidase, the HD1 and SiPRR37 genes controlling heading time, the Sh1 and SvLes1 genes involved in grain shattering, and the C gene controlling leaf sheath pigmentation), and the variation and distribution of these genes suggested complex patterns of evolution under human and/or natural selection.
Collapse
Affiliation(s)
- Kenji Fukunaga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara 727-0023, Japan
| | - Makoto Kawase
- Faculty of Agriculture, Tokyo University of Agriculture, Atsugi 243-0034, Japan
| |
Collapse
|
3
|
Niu J, Guan Y, Yu X, Wang R, Qin L, Chen E, Yang Y, Zhang H, Wang H, Li F. SiNF-YC2 Regulates Early Maturity and Salt Tolerance in Setaria italica. Int J Mol Sci 2023; 24:ijms24087217. [PMID: 37108376 PMCID: PMC10138326 DOI: 10.3390/ijms24087217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/07/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
Early maturity is an important agronomic trait in most crops, because it can solve the problem of planting in stubble for multiple cropping as well as make full use of light and temperature resources in alpine regions, thereby avoiding damage from low temperatures in the early growth period and early frost damage in the late growth period to improve crop yield and quality. The expression of genes that determine flowering affects flowering time, which directly affects crop maturity and indirectly affects crop yield and quality. Therefore, it is important to analyze the regulatory network of flowering for the cultivation of early-maturing varieties. Foxtail millet (Setaria italica) is a reserve crop for future extreme weather and is also a model crop for functional gene research in C4 crops. However, there are few reports on the molecular mechanism regulating flowering in foxtail millet. A putative candidate gene, SiNF-YC2, was isolated based on quantitative trait loci (QTL) mapping analysis. Bioinformatics analysis showed that SiNF-YC2 has a conserved HAP5 domain, which indicates that it is a member of the NF-YC transcription factor family. The promoter of SiNF-YC2 contains light-response-, hormone-, and stress-resistance-related elements. The expression of SiNF-YC2 was sensitive to the photoperiod and was related to the regulation of biological rhythm. Expression also varied in different tissues and in response to drought and salt stress. In a yeast two-hybrid assay, SiNF-YC2 interacted with SiCO in the nucleus. Functional analysis suggested that SiNF-YC2 promotes flowering and improves resistance to salt stress.
Collapse
Affiliation(s)
- Jiahong Niu
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- College of Life Science, Shandong Normal University, Jinan 250358, China
| | - Yanan Guan
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiao Yu
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- College of Life Science, Shandong Normal University, Jinan 250358, China
| | - Runfeng Wang
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ling Qin
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Erying Chen
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yanbing Yang
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Huawen Zhang
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Hailian Wang
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Feifei Li
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| |
Collapse
|
4
|
Huang YC, Wang YT, Choong YC, Huang HY, Chen YR, Hsieh TF, Lin YR. How ambient temperature affects the heading date of foxtail millet ( Setaria italica). FRONTIERS IN PLANT SCIENCE 2023; 14:1147756. [PMID: 36938030 PMCID: PMC10018198 DOI: 10.3389/fpls.2023.1147756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Foxtail millet (Setaria italica), a short-day plant, is one of the important crops for food security encountering climate change, particularly in regions where it is a staple food. Under the short-day condition in Taiwan, the heading dates (HDs) of foxtail millet accessions varied by genotypes and ambient temperature (AT). The allelic polymorphisms in flowering time (FT)-related genes were associated with HD variations. AT, in the range of 13°C-30°C that was based on field studies at three different latitudes in Taiwan and observations in the phytotron at four different AT regimes, was positively correlated with growth rate, and high AT promoted HD. To elucidate the molecular mechanism of foxtail millet HD, the expression of 14 key FT-related genes in four accessions at different ATs was assessed. We found that the expression levels of SiPRR95, SiPRR1, SiPRR59, SiGhd7-2, SiPHYB, and SiGhd7 were negatively correlated with AT, whereas the expression levels of SiEhd1, SiFT11, and SiCO4 were positively correlated with AT. Furthermore, the expression levels of SiGhd7-2, SiEhd1, SiFT, and SiFT11 were significantly associated with HD. A coexpression regulatory network was identified that shown genes involved in the circadian clock, light and temperature signaling, and regulation of flowering, but not those involved in photoperiod pathway, interacted and were influenced by AT. The results reveal how gene × temperature and gene × gene interactions affect the HD in foxtail millet and could serve as a foundation for breeding foxtail millet cultivars for shift production to increase yield in response to global warming.
Collapse
Affiliation(s)
- Ya-Chen Huang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yu-tang Wang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yee-ching Choong
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Hsin-ya Huang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yu-ru Chen
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Yann-rong Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
- Headquarters, World Vegetable Center, Tainan, Taiwan
| |
Collapse
|
5
|
Li C, Ma J, Wang G, Li H, Wang H, Wang G, Jiang Y, Liu Y, Liu G, Liu G, Cheng R, Wang H, Wei J, Yao L. Exploring the SiCCT Gene Family and Its Role in Heading Date in Foxtail Millet. FRONTIERS IN PLANT SCIENCE 2022; 13:863298. [PMID: 35755676 PMCID: PMC9218912 DOI: 10.3389/fpls.2022.863298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
CCT transcription factors are involved in the regulation of photoperiod and abiotic stress in Arabidopsis and rice. It is not clear that how CCT gene family expand and regulate heading date in foxtail millet. In this study, we conducted a systematic analysis of the CCT gene family in foxtail millet. Thirty-nine CCT genes were identified and divided into four subfamilies based on functional motifs. Analysis showed that dispersed duplication played a predominant role in the expansion of CCT genes during evolution. Nucleotide diversity analysis suggested that genes in CONSTANS (COL)-like, CCT MOTIF FAMILY (CMF)-like, and pseudoresponse response regulator (PRR)-like subfamilies were subjected to selection. Fifteen CCT genes were colocalized with previous heading date quantitative trait loci (QTL) and genome-wide association analysis (GWAS) signals. Transgenic plants were then employed to confirm that overexpression of the CCT gene SiPRR37 delayed the heading date and increased plant height. Our study first investigated the characterization and expansion of the CCT family in foxtail millet and demonstrated the role of SiPRR37. These results lay a significant foundation for further research on the function of CCT genes and provide a cue for the regulation of heading date.
Collapse
Affiliation(s)
- Congcong Li
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Ma
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Vegetable Research, Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, China
| | - Genping Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Hailong Wang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Guoliang Wang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Yanmiao Jiang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yanan Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guiming Liu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhua Wei
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Lei Yao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| |
Collapse
|
6
|
Recombinant inbred lines and next-generation sequencing enable rapid identification of candidate genes involved in morphological and agronomic traits in foxtail millet. Sci Rep 2022; 12:218. [PMID: 34997038 PMCID: PMC8742101 DOI: 10.1038/s41598-021-04012-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
We constructed recombinant inbred lines (RILs) between a Japanese and a Taiwanese landrace of foxtail millet and employed next-generation sequencing, such as flexible ddRAD-seq and Nanopore sequencing to identify the candidate genes involved in the crop evolution of foxtail millet. We successfully constructed a linkage map using flexible ddRAD-seq with parents and RILs and detected major QTLs for each of three traits: leaf sheath colors, spikelet-tipped bristles (stb), and days to heading (DTH). (1) For leaf sheath colors, we identified the C gene on chromosome IV. (2) We identified a homeobox (HOX14) gene for stb on chromosome II, which shows homology with HvVrs1 in barley. (3) Finally, we identified a QTL with a large effect on DTH on chromosome II. A parent of the RILs from Taiwan and Yugu1 had a Harbinger-like TE in intron 3 of this gene. We also investigated the geographical distribution of the TE insertion type of this gene and found that the insertion type is distributed in the northern part of East Asia and intensively in South and Southeast Asia, suggesting that loss/reduction of function of this gene plays an important role in spreading into the northern part of East Asia and subtropical and tropical zones.
Collapse
|
7
|
Li FF, Niu JH, Yu X, Kong QH, Wang RF, Qin L, Chen EY, Yang YB, Liu ZY, Lang LN, Zhang HW, Wang HL, Guan YA. Isolation and identification of SiCOL5, which is involved in photoperiod response, based on the quantitative trait locus mapping of Setaria italica. FRONTIERS IN PLANT SCIENCE 2022; 13:969604. [PMID: 36204051 PMCID: PMC9530826 DOI: 10.3389/fpls.2022.969604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/16/2022] [Indexed: 05/13/2023]
Abstract
Foxtail millet (Setaria italica) is a versatile grain and fodder crop grown in arid and semi-arid regions. It is an especially important crop for combating malnutrition in certain poverty-stricken areas of the world. Photoperiod sensitivity is a major constraint to the distribution and utilization of foxtail millet germplasm resources. Foxtail millet may be suitable as a model species for studying the photoperiod sensitivity of C4 crops. However, the genetic basis of the photoperiod response of foxtail millet remains poorly studied. To detect the genetic basis of photoperiod sensitivity-related traits, a recombinant inbred line (RIL) population consisting of 313 lines derived from a cross between the spring-sown cultivar "Longgu 3" and the summer-sown cultivar "Canggu 3" was established. The RIL population was genotyped using whole-genome re-sequencing and was phenotyped in four environments. A high-density genetic linkage map was constructed with an average distance between adjacent markers of 0.69 cM. A total of 21 quantitative trait loci (QTLs) were identified by composite interval mapping, and 116 candidate genes were predicted according to gene annotations and variations between parents, among which three genes were considered important candidate genes by the integration and overall consideration of the results from gene annotation, SNP and indel analysis, cis-element analysis, and the expression pattern of different genes in different varieties, which have different photoperiod sensitivities. A putative candidate gene, SiCOL5, was isolated based on QTL mapping analysis. The expression of SiCOL5 was sensitive to photoperiod and was regulated by biological rhythm-related genes. Function analysis suggested that SiCOL5 positively regulated flowering time. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that SiCOL5 was capable of interacting with SiNF-YA1 in the nucleus.
Collapse
Affiliation(s)
- Fei-fei Li
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jia-hong Niu
- College of Life Science, Shandong Normal University, Jinan, China
| | - Xiao Yu
- College of Life Science, Shandong Normal University, Jinan, China
| | - Qing-hua Kong
- College of Life Science, Shandong Normal University, Jinan, China
| | - Run-feng Wang
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ling Qin
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Er-ying Chen
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yan-bing Yang
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhen-yu Liu
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Li-na Lang
- Shandong Seed Administration Station, Jinan, China
| | - Hua-wen Zhang
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hai-lian Wang
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yan-an Guan
- Featured Crops Engineering Laboratory of Shandong Province, National Engineering Research Center of Wheat and Maize, Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- *Correspondence: Yan-an Guan,
| |
Collapse
|
8
|
Li C, Wang G, Li H, Wang G, Ma J, Zhao X, Huo L, Zhang L, Jiang Y, Zhang J, Liu G, Liu G, Cheng R, Wei J, Yao L. High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1303-1317. [PMID: 33566123 DOI: 10.1007/s00122-020-03760-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/30/2020] [Indexed: 05/20/2023]
Abstract
Based on the high-density variation map, we identified genome-level evidence for local adaptation and demonstrated that Siprr37 with transposon insertion contributes to the fitness of foxtail millet in the northeastern ecoregion. Adaptation is a robust way through which plants are able to overcome environmental constraints. The mechanisms of adaptation in heterogeneous natural environments are largely unknown. Deciphering the genomic basis of local adaptation will contribute to further improvement in domesticated plants. To this end, we describe a high-depth (19.4 ×) haplotype map of 3.02 million single nucleotide polymorphisms in foxtail millet (Setaria italica) from whole-genome resequencing of 312 accessions. In the genome-wide scan, we identified a set of improvement signals (including the homologous gene of OsIPA1, a key gene controlling ideal plant architecture) related to the geographical adaptation to four ecoregions in China. In particular, based on the genome-wide association analysis results, we identified the contribution of a pseudo-response regulator gene, SiPRR37, to heading date adaptation in foxtail millet. We observed the expression changes of SiPRR37 resulted from a key Tc1-Mariner transposon insertion in the first intron. Positive selection analyses revealed that SiPRR37 mainly contributed to the adaptation of northeastern ecoregions. Taken together, foxtail millet adapted to the northeastern region by regulating the function of SiPRR37, which sheds lights on genome-level evidence for adaptive geographical divergence. Besides, our data provide a nearly complete catalog of genomic variation aiding the identification of functionally important variants.
Collapse
Affiliation(s)
- Congcong Li
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Genping Wang
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Haiquan Li
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Guoliang Wang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jian Ma
- Beijing Vegetable Research Center, Beijing Key Laboratory of Vegetable Germplasms Improvement, National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xin Zhao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Linhe Huo
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Liquan Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yanmiao Jiang
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Jiewei Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Guiming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Guoqing Liu
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Ruhong Cheng
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Jianhua Wei
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Lei Yao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| |
Collapse
|
9
|
Hunt HV, Przelomska NAS, Campana MG, Cockram J, Bligh HFJ, Kneale CJ, Romanova OI, Malinovskaya EV, Jones MK. Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping-by-sequencing. THE PLANT GENOME 2021; 14:e20081. [PMID: 33543599 PMCID: PMC8638668 DOI: 10.1002/tpg2.20081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 05/11/2023]
Abstract
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.
Collapse
Affiliation(s)
- Harriet V. Hunt
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Natalia A. S. Przelomska
- Comparative Plant and Fungal BiologyRoyal Botanic GardensKewRichmondTW9 3AEUK
- Department of AnthropologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDC20560USA
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
| | - Michael G. Campana
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
| | - James Cockram
- The John Bingham LaboratoryNIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
| | | | - Catherine J. Kneale
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Olga I. Romanova
- N.I. Vavilov Institute of Plant Genetic Resources (VIR)St. Petersburg190000Russia
| | | | - Martin K. Jones
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
| |
Collapse
|
10
|
Jensen E, Shafiei R, Ma X, Serba DD, Smith DP, Slavov GT, Robson P, Farrar K, Thomas Jones S, Swaller T, Flavell R, Clifton‐Brown J, Saha MC, Donnison I. Linkage mapping evidence for a syntenic QTL associated with flowering time in perennial C 4 rhizomatous grasses Miscanthus and switchgrass. GLOBAL CHANGE BIOLOGY. BIOENERGY 2021; 13:98-111. [PMID: 33381230 PMCID: PMC7756372 DOI: 10.1111/gcbb.12755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/10/2020] [Indexed: 06/12/2023]
Abstract
Flowering in perennial species is directed via complex signalling pathways that adjust to developmental regulations and environmental cues. Synchronized flowering in certain environments is a prerequisite to commercial seed production, and so the elucidation of the genetic architecture of flowering time in Miscanthus and switchgrass could aid breeding in these underdeveloped species. In this context, we assessed a mapping population in Miscanthus and two ecologically diverse switchgrass mapping populations over 3 years from planting. Multiple flowering time quantitative trait loci (QTL) were identified in both species. Remarkably, the most significant Miscanthus and switchgrass QTL proved to be syntenic, located on linkage groups 4 and 2, with logarithm of odds scores of 17.05 and 21.8 respectively. These QTL regions contained three flowering time transcription factors: Squamosa Promoter-binding protein-Like, MADS-box SEPELLATA2 and gibberellin-responsive bHLH137. The former is emerging as a key component of the age-related flowering time pathway.
Collapse
Affiliation(s)
- Elaine Jensen
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Reza Shafiei
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- University of Dundee at JHIDundeeUK
| | - Xue‐Feng Ma
- Ceres, Inc.Thousand OaksCAUSA
- Noble Research Institute, LLC.ArdmoreOKUSA
| | - Desalegn D. Serba
- Noble Research Institute, LLC.ArdmoreOKUSA
- Agricultural Research Center‐HaysKansas State UniversityHaysKSUSA
| | - Daniel P. Smith
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- ScionRotoruaNew Zealand
| | - Gancho T. Slavov
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- ScionRotoruaNew Zealand
| | - Paul Robson
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Kerrie Farrar
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Sian Thomas Jones
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Timothy Swaller
- Ceres, Inc.Thousand OaksCAUSA
- Genomics Institute of the Novartis Research FoundationSan DiegoCAUSA
| | - Richard Flavell
- Ceres, Inc.Thousand OaksCAUSA
- International Wheat Yield PartnershipTexas A&M UniversityCollege StationTXUSA
| | - John Clifton‐Brown
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | - Iain Donnison
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| |
Collapse
|
11
|
Renganathan VG, Vanniarajan C, Karthikeyan A, Ramalingam J. Barnyard Millet for Food and Nutritional Security: Current Status and Future Research Direction. Front Genet 2020; 11:500. [PMID: 32655612 PMCID: PMC7325689 DOI: 10.3389/fgene.2020.00500] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/22/2020] [Indexed: 01/09/2023] Open
Abstract
Barnyard millet (Echinochloa species) has become one of the most important minor millet crops in Asia, showing a firm upsurge in world production. The genus Echinochloa comprises of two major species, Echinochloa esculenta and Echinochloa frumentacea, which are predominantly cultivated for human consumption and livestock feed. They are less susceptible to biotic and abiotic stresses. Barnyard millet grain is a good source of protein, carbohydrate, fiber, and, most notably, contains more micronutrients (iron and zinc) than other major cereals. Despite its nutritional and agronomic benefits, barnyard millet has remained an underutilized crop. Over the past decades, very limited attempts have been made to study the features of this crop. Hence, more concerted research efforts are required to characterize germplasm resources, identify trait-specific donors, develop mapping population, and discover QTL/gene (s). The recent release of genome and transcriptome sequences of wild and cultivated Echinochloa species, respectively has facilitated in understanding the genetic architecture and decoding the rapport between genotype and phenotype of micronutrients and agronomic traits in this crop. In this review, we highlight the importance of barnyard millet in the current scenario and discuss the up-to-date status of genetic and genomics research and the research gaps to be worked upon by suggesting directions for future research to make barnyard millet a potential crop in contributing to food and nutritional security.
Collapse
Affiliation(s)
- Vellaichamy Gandhimeyyan Renganathan
- Department of Plant Breeding and Genetics, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Chockalingam Vanniarajan
- Department of Plant Breeding and Genetics, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Adhimoolam Karthikeyan
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Jegadeesan Ramalingam
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| |
Collapse
|
12
|
QTL mapping of yield component traits on bin map generated from resequencing a RIL population of foxtail millet (Setaria italica). BMC Genomics 2020; 21:141. [PMID: 32041544 PMCID: PMC7011527 DOI: 10.1186/s12864-020-6553-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 02/04/2020] [Indexed: 01/19/2023] Open
Abstract
Background Foxtail millet (Setaria italica) has been developed into a model genetical system for deciphering architectural evolution, C4 photosynthesis, nutritional properties, abiotic tolerance and bioenergy in cereal grasses because of its advantageous characters with the small genome size, self-fertilization, short growing cycle, small growth stature, efficient genetic transformation and abundant diverse germplasm resources. Therefore, excavating QTLs of yield component traits, which are closely related to aspects mentioned above, will further facilitate genetic research in foxtail millet and close cereal species. Results Here, 164 Recombinant inbreed lines from a cross between Longgu7 and Yugu1 were created and 1,047,978 SNPs were identified between both parents via resequencing. A total of 3413 bin markers developed from SNPs were used to construct a binary map, containing 3963 recombinant breakpoints and totaling 1222.26 cM with an average distance of 0.36 cM between adjacent markers. Forty-seven QTLs were identified for four traits of straw weight, panicle weight, grain weight per plant and 1000-grain weight. These QTLs explained 5.5–14.7% of phenotypic variance. Thirty-nine favorable QTL alleles were found to inherit from Yugu1. Three stable QTLs were detected in multi-environments, and nine QTL clusters were identified on Chromosome 3, 6, 7 and 9. Conclusions A high-density genetic map with 3413 bin markers was constructed and three stable QTLs and 9 QTL clusters for yield component traits were identified. The results laid a powerful foundation for fine mapping, identifying candidate genes, elaborating molecular mechanisms and application in foxtail millet breeding programs by marker-assisted selection.
Collapse
|
13
|
Jaiswal V, Gupta S, Gahlaut V, Muthamilarasan M, Bandyopadhyay T, Ramchiary N, Prasad M. Genome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing. Sci Rep 2019; 9:5020. [PMID: 30903013 PMCID: PMC6430830 DOI: 10.1038/s41598-019-41602-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/05/2019] [Indexed: 12/17/2022] Open
Abstract
Foxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association study (GWAS) was performed for ten important agronomic traits in 142 foxtail millet core eco-geographically diverse genotypes using 10 K SNPs developed through GBS-ddRAD approach. Number of SNPs on individual chromosome ranged from 844 (chromosome 5) to 2153 (chromosome 8) with an average SNP frequency of 25.9 per Mb. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations was found to decay rapidly with the genetic distance of 177 Kb. However, for individual chromosome, LD decay distance ranged from 76 Kb (chromosome 6) to 357 Kb (chromosome 4). GWAS identified 81 MTAs (marker-trait associations) for ten traits across the genome. High confidence MTAs for three important agronomic traits including FLW (flag leaf width), GY (grain yield) and TGW (thousand-grain weight) were identified. Significant pyramiding effect of identified MTAs further supplemented its importance in breeding programs. Desirable alleles and superior genotypes identified in the present study may prove valuable for foxtail millet improvement through marker-assisted selection.
Collapse
Affiliation(s)
- Vandana Jaiswal
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sarika Gupta
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Mehanathan Muthamilarasan
- National Institute of Plant Genome Research, New Delhi, 110067, India
- ICAR-National Research Centre on Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi, 110012, India
| | | | - Nirala Ramchiary
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, 110067, India.
| |
Collapse
|
14
|
Taylor M, Tornqvist CE, Zhao X, Grabowski P, Doerge R, Ma J, Volenec J, Evans J, Ramstein GP, Sanciangco MD, Buell CR, Casler MD, Jiang Y. Genome-Wide Association Study in Pseudo-F 2 Populations of Switchgrass Identifies Genetic Loci Affecting Heading and Anthesis Dates. FRONTIERS IN PLANT SCIENCE 2018; 9:1250. [PMID: 30271414 PMCID: PMC6146286 DOI: 10.3389/fpls.2018.01250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 08/06/2018] [Indexed: 06/01/2023]
Abstract
Switchgrass (Panicum virgatum) is a native prairie grass and valuable bio-energy crop. The physiological change from juvenile to reproductive adult can draw important resources away from growth into producing reproductive structures, thereby limiting the growth potential of early flowering plants. Delaying the flowering of switchgrass is one approach by which to increase total biomass. The objective of this research was to identify genetic variants and candidate genes for controlling heading and anthesis in segregating switchgrass populations. Four pseudo-F2 populations (two pairs of reciprocal crosses) were developed from lowland (late flowering) and upland (early flowering) ecotypes, and heading and anthesis dates of these populations were collected in Lafayette, IN and DeKalb, IL in 2015 and 2016. Across 2 years, there was a 34- and 73-day difference in heading and a 52- and 75-day difference in anthesis at the Lafayette and DeKalb locations, respectively. A total of 37,901 single nucleotide polymorphisms obtained by exome capture sequencing of the populations were used in a genome-wide association study (GWAS) that identified five significant signals at three loci for heading and two loci for anthesis. Among them, a homolog of FLOWERING LOCUS T on chromosome 5b associated with heading date was identified at the Lafayette location across 2 years. A homolog of ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5, a light modulator in the circadian clock associated with heading date was detected on chromosome 8a across locations and years. These results demonstrate that genetic variants related to floral development could lend themselves to a long-term goal of developing late flowering varieties of switchgrass with high biomass yield.
Collapse
Affiliation(s)
- Megan Taylor
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Carl-Erik Tornqvist
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Xiongwei Zhao
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Paul Grabowski
- U.S. Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service, Madison, WI, United States
| | - Rebecca Doerge
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
- Department of Biology and Department of Statistics, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Jeffrey Volenec
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Joseph Evans
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Guillaume P. Ramstein
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Millicent D. Sanciangco
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - C. Robin Buell
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Michael D. Casler
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
- U.S. Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service, Madison, WI, United States
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| |
Collapse
|
15
|
Chaluvadi S, Bennetzen JL. Species-Associated Differences in the Below-Ground Microbiomes of Wild and Domesticated Setaria. FRONTIERS IN PLANT SCIENCE 2018; 9:1183. [PMID: 30186294 PMCID: PMC6111228 DOI: 10.3389/fpls.2018.01183] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/24/2018] [Indexed: 05/08/2023]
Abstract
The rhizosphere microbiome is known to play a crucial role in promoting plant growth, partly by countering soil-borne phytoparasites and by improving nutrient uptake. The abundance and composition of the rhizosphere and root-associated microbiota are influenced by several factors, including plant species and genotype. We hypothesize that crop domestication might influence the composition and diversity of plant-associated microbiomes. We tested the contribution of domestication to the bacterial and archaeal root and soil composition associated with six genotypes of domesticated Setaria italica and four genotypes of its wild ancestor, S. viridis. The bacterial microbiome in the rhizoplane and root endophyte compartments, and the archaea in the endophyte compartment, showed major composition differences. For instance, members of the Betaproteobacteria and Firmicutes were overrepresented in S. italica root samples compared to S. viridis. Metagenomic analysis of samples that contained both root surface-bound (rhizoplane) and inside-root (endophytic) bacteria defined two unique microbial communities only associated with S. italica roots and one only associated with S. viridis roots. Root endophytic bacteria were found in six discernible communities, of which four were primarily on S. italica and two primarily on S. viridis. Among archaea, Methanobacteria, and Methanomicrobia exhibited species-associated differences in the rhizosphere and root compartments, but most detected archaea were not classified more specifically than at the level of phylum. These results indicate a host genetic contribution to the microbial composition in Setaria, and suggest that domestication has selected for specific associations in the root and in the rhizosphere.
Collapse
|
16
|
Tornqvist CE, Taylor M, Jiang Y, Evans J, Buell CR, Kaeppler SM, Casler MD. Quantitative Trait Locus Mapping for Flowering Time in a Lowland × Upland Switchgrass Pseudo-F2 Population. THE PLANT GENOME 2018; 11. [PMID: 30025023 DOI: 10.3835/plantgenome2017.10.0093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Flowering is an important developmental event in switchgrass (), as the time to complete the life cycle affects overall biomass accumulation. The objective of this study was to generate a linkage map using single nucleotide polymorphism (SNP) markers to identify quantitative trait loci (QTL) associated with flowering time. A pseudo-F population was created by crossing two siblings derived from an initial cross between the lowland population Ellsworth and the upland cultivar Summer. Heading and anthesis dates were collected for 2 yr at two locations: DeKalb, IL and Lafayette, IN. Nine QTL for flowering time were detected, two of which were heading-associated, four anthesis-associated, and three associated with both heading and anthesis. One QTL on linkage group (LG) 2a was detected for heading and anthesis in each location and year when environments were analyzed separately, and in a combined analysis across both locations and years. The effect on heading and anthesis of the QTL on LG 2a ranged from 4 to 13 and 5 to 9 d, respectively, depending on environment. Our findings validate QTL for switchgrass flowering time from previous research and identified additional QTL. Based on the switchgrass reference genome version 1.1, flowering time gene homologs reside near the LG 2a QTL and include PSEUDO RESPONSE REGULATOR 5, SUPPRESSOR OF FRIGIDA 4, and APETALA 1, respectively involved in the circadian clock, vernalization, and floral meristem identity. Markers linked to the QTL can be used to improve the efficiency of breeding switchgrass for delayed flowering to increase biomass yield.
Collapse
|
17
|
Wang X, Yang S, Chen Y, Zhang S, Zhao Q, Li M, Gao Y, Yang L, Bennetzen JL. Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana. BMC Genomics 2018; 19:500. [PMID: 29945549 PMCID: PMC6020451 DOI: 10.1186/s12864-018-4878-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 06/18/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Simple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breeding. In the model plants in Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR content has become possible now because several Nicotiana genomes have been sequenced. We conducted a genome-wide SSR characterization and marker development across seven Nicotiana genomes. RESULTS Here, we initially characterized 2,483,032 SSRs (repeat units of 1-10 bp) from seven genomic sequences of Nicotiana and developed SSR markers using the GMATA® software package. Of investigated repeat units, mono-, di- and tri-nucleotide SSRs account for 98% of all SSRs in Nicotiana. More complex SSR motifs, although rare, are highly variable between Nicotiana genomes. A total of 1,224,048 non-redundant Nicotiana (NIX) markers were developed, of which 99.98% are novel. An efficient and uniform genotyping protocol for NIX markers was developed and validated. We created a web-based database of NIX marker information including amplicon sizes of alleles in each genome for downloading and online analysis. CONCLUSIONS The present work constitutes the first deep characterization of SSRs in seven genomes of Nicotiana, and the development of NIX markers for these SSRs. Our online marker database and an efficient genotyping protocol facilitate the application of these markers. The NIX markers greatly expand Nicotiana marker resources, thus providing a useful tool for future research and breeding. We demonstrate a novel protocol for SSR marker development and utilization at the whole genome scale that can be applied to any lineage of organisms. The Tobacco Markers & Primers Database (TMPD) is available at http://biodb.sdau.edu.cn/tmpd/index.html.
Collapse
Affiliation(s)
- Xuewen Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
| | - Shuai Yang
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 China
| | - Yongdui Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650223 People’s Republic of China
| | - Shumeng Zhang
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
| | - Qingshi Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
| | - Meng Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
| | - Yulong Gao
- Tobacco Breeding Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021 Yunnan China
| | - Long Yang
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 China
| | - Jeffrey L. Bennetzen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 People’s Republic of China
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
| |
Collapse
|
18
|
Hu H, Mauro-Herrera M, Doust AN. Domestication and Improvement in the Model C4 Grass, Setaria. FRONTIERS IN PLANT SCIENCE 2018; 9:719. [PMID: 29896214 PMCID: PMC5986938 DOI: 10.3389/fpls.2018.00719] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 05/14/2018] [Indexed: 05/17/2023]
Abstract
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.
Collapse
Affiliation(s)
| | | | - Andrew N. Doust
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, United States
| |
Collapse
|
19
|
Xie Y, Wang X. Comparative transcriptomic analysis identifies genes responsible for fruit count and oil yield in the oil tea plant Camellia chekiangoleosa. Sci Rep 2018; 8:6637. [PMID: 29703942 PMCID: PMC5923238 DOI: 10.1038/s41598-018-24073-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/21/2018] [Indexed: 12/02/2022] Open
Abstract
Fruit yield is an important trait for horticultural crops. However, the limited fruit yield of Camellia chekiangoleosa, a novel promising oil tree, restricts the production of oil. The breeding improvement is little due to its long generation time and lack of available genomic sequence. We identified distinct fruit count phenotypes, high-yield (HY) and low-yield (LY). To understand the underlying genetic basis, we focused on global gene discovery and expression levels in floral buds, which affect fruit count. A total of 140,299 de novo assembled unigenes were obtained using RNA-seq technology, and more genes were expressed in HY than in LY. 2395 differentially expressed genes (DEGs) were identified and enriched in membrane, energy metabolism, secondary metabolism, fatty acid biosynthesis and metabolism, and 18 other metabolic pathways. Of the DEGs, twelve identified transcription factors, including AP2, mostly involve in inflorescence and flower development and in hormone networks. Key DEGs in fatty acid biosynthesis (Fab) FabB, FabF, FabZ, and AccD were highly expressed in floral buds and associated with high oil yield in fruits. We hypothesized that a potential link exists between fruit count and its oil yield. These findings help to elucidate the molecular cues affecting fruit count and oil yield.
Collapse
Affiliation(s)
- Yun Xie
- Jiyang College, Zhejiang A&F University, Zhuji, Zhejiang, 311800, China
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, 30602, USA.
| |
Collapse
|
20
|
Lai X, Yan L, Lu Y, Schnable JC. Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:843-855. [PMID: 29265526 DOI: 10.1111/tpj.13806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/27/2017] [Accepted: 12/04/2017] [Indexed: 05/14/2023]
Abstract
The domestication of diverse grain crops from wild grasses was a result of artificial selection for a suite of overlapping traits producing changes referred to in aggregate as 'domestication syndrome'. Parallel phenotypic change can be accomplished by either selection on orthologous genes or selection on non-orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many 'classic' domestication genes identified through quantitative trait locus mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization part of domestication targeted small and largely non-overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.
Collapse
Affiliation(s)
- Xianjun Lai
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lang Yan
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
- Laboratory of Functional Genome and Application of Potato, Xichang College, Liangshan, 615000, China
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - James C Schnable
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, NE, 68588, USA
| |
Collapse
|
21
|
Desai JS, Slabaugh E, Liebelt DJ, Fredenberg JD, Gray BN, Jagadish SVK, Wilkins O, Doherty CJ. Neural Net Classification Combined With Movement Analysis to Evaluate Setaria viridis as a Model System for Time of Day of Anther Appearance. FRONTIERS IN PLANT SCIENCE 2018; 9:1585. [PMID: 30429868 PMCID: PMC6220418 DOI: 10.3389/fpls.2018.01585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 10/11/2018] [Indexed: 05/13/2023]
Abstract
In many plant species, the time of day at which flowers open to permit pollination is tightly regulated. Proper time of flower opening, or Time of Day of Anther Appearance (TAA), may coordinate flowering opening with pollinator activity or may shift temperature sensitive developmental processes to cooler times of the day. The genetic mechanisms that regulate the timing of this process in cereal crops are unknown. To address this knowledge gap, it is necessary to establish a monocot model system that exhibits variation in TAA. Here, we examine the suitability of Setaria viridis, the model for C4 photosynthesis, for such a role. We developed an imaging system to monitor the temporal regulation of growth, flower opening time, and other physiological characteristics in Setaria. This system enabled us to compare Setaria varieties Ames 32254, Ames 32276, and PI 669942 variation in growth and daily flower opening time. We observed that TAA occurs primarily at night in these three Setaria accessions. However, significant variation between the accessions was observed for both the ratio of flowers that open in the day vs. night and the specific time of day where the rate is maximal. Characterizing this physiological variation is a requisite step toward uncovering the molecular mechanisms regulating TAA. Leveraging the regulation of TAA could provide researchers with a genetic tool to improve crop productivity in new environments.
Collapse
Affiliation(s)
- Jigar S. Desai
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Erin Slabaugh
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Donna J. Liebelt
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Jacob D. Fredenberg
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | | | | | - Olivia Wilkins
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Colleen J. Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Colleen J. Doherty
| |
Collapse
|
22
|
Yoshitsu Y, Takakusagi M, Abe A, Takagi H, Uemura A, Yaegashi H, Terauchi R, Takahata Y, Hatakeyama K, Yokoi S. QTL-seq analysis identifies two genomic regions determining the heading date of foxtail millet, Setaria italica (L.) P.Beauv. BREEDING SCIENCE 2017; 67:518-527. [PMID: 29398946 PMCID: PMC5790050 DOI: 10.1270/jsbbs.17061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/30/2017] [Indexed: 05/29/2023]
Abstract
Heading date is an important event to ensure successful seed production. Although foxtail millet (Setaria italica (L.) P.Beauv.) is an important foodstuff in semiarid regions around the world, the genetic basis determining heading date is unclear. To identify genomic regions regulating days to heading (DTH), we conducted a QTL-seq analysis based on combining whole-genome re-sequencing and bulked-segregant analysis of an F2 population derived from crosses between the middle-heading cultivar Shinanotsubuhime and the early-heading cultivar Yuikogane. Under field conditions, transgressive segregation of DTH toward late heading was observed in the F2 population. We made three types of bulk samples: Y-bulk (early-heading), S-bulk (late-heading) and L-bulk (extremely late-heading). By genome-wide comparison of SNPs in the Y-bulk vs. the S-bulk and the Y-bulk vs. the L-bulk, we identified two QTLs associated with DTH. The first QTL, qDTH2, was detected on chromosome 2 from the Y-bulk and S-bulk comparison. The second QTL, qDTH7, was detected on chromosome 7 from the Y-bulk and L-bulk comparison. The Shinanotsubuhime allele for qDTH2 caused late heading in the F2 population, whereas the Yuikogane allele for qDTH7 led to extremely late heading. These results suggest that allelic differences in both qDTH2 and qDTH7 determine regional adaptability in S. italica.
Collapse
Affiliation(s)
- Yuki Yoshitsu
- Faculty of Agriculture, Iwate University,
Morioka, Iwate 020-8550,
Japan
| | - Masato Takakusagi
- Kenpoku Agricultural Research Institute, Iwate Agricultural Research Center,
Karumai, Iwate 028-6222,
Japan
| | - Akira Abe
- Iwate Biotechnology Research Center,
Kitakami, Iwate 024-0003,
Japan
| | - Hiroki Takagi
- Iwate Biotechnology Research Center,
Kitakami, Iwate 024-0003,
Japan
- Ishikawa Prefectural University,
Nonoichi, Ishikawa 921-8836,
Japan
| | - Aiko Uemura
- Iwate Biotechnology Research Center,
Kitakami, Iwate 024-0003,
Japan
| | - Hiroki Yaegashi
- Iwate Biotechnology Research Center,
Kitakami, Iwate 024-0003,
Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center,
Kitakami, Iwate 024-0003,
Japan
| | - Yoshihito Takahata
- Faculty of Agriculture, Iwate University,
Morioka, Iwate 020-8550,
Japan
| | | | - Shuji Yokoi
- Faculty of Agriculture, Iwate University,
Morioka, Iwate 020-8550,
Japan
- Graduate School of Life and Environmental Science, Osaka Prefecture University,
Sakai, Osaka 599-8531,
Japan
| |
Collapse
|
23
|
Feldman MJ, Paul RE, Banan D, Barrett JF, Sebastian J, Yee MC, Jiang H, Lipka AE, Brutnell TP, Dinneny JR, Leakey ADB, Baxter I. Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria. PLoS Genet 2017. [PMID: 28644860 PMCID: PMC5507400 DOI: 10.1371/journal.pgen.1006841] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor height throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by growth environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the major genetic loci that influence plant height function independent of growth environment. The identity and contribution of loci that influence height changes dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in Setaria. In this population, alleles inherited from the weedy S. viridis parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated S. italica parent collectively act to increase plant height later in development. Growth is a dynamic process that responds to a changing environment. Most of the methods that we have for measuring are static and collecting information throughout an organisms lifecycle is labor and cost prohibitive. Advances in imaging and robotics technology have enabled novel approaches to understanding how plants adapt to the environment. Using the model grass Setaria and new methods for measuring parameters from images, we investigate the genetic architecture of plant height in response to water availability and planting density. Height is one of the most influential components of plant architecture, determining tradeoffs between competition and resource allocation and is an important trait for boosting yields. The non-destructive nature of plant height measurements has enabled us to monitor growth throughout the plant life cycle in both field and controlled environments. We identified several loci controlling height in a population derived from a wild strain of Setaria viridis and its domesticated relative Setaria italica, as well as the developmental time in which these loci act. In this population, alleles inherited from the wild parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated parent collectively act to increase plant height later in development.
Collapse
Affiliation(s)
- Max J. Feldman
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Rachel E. Paul
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Darshi Banan
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jennifer F. Barrett
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Jose Sebastian
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - Muh-Ching Yee
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - Hui Jiang
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Thomas P. Brutnell
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - José R. Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - Andrew D. B. Leakey
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- USDA-ARS, Plant Genetics Research Unit, St. Louis, Missouri, United States of America
- * E-mail:
| |
Collapse
|
24
|
Wang J, Wang Z, Du X, Yang H, Han F, Han Y, Yuan F, Zhang L, Peng S, Guo E. A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq. PLoS One 2017. [PMID: 28644843 PMCID: PMC5482450 DOI: 10.1371/journal.pone.0179717] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Jun Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
- * E-mail: (JW); (EG)
| | - Zhilan Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Xiaofen Du
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Huiqing Yang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Fang Han
- Research Institute of Agriculture Sciences of Yanan, Yanan, Shaanxi, China
| | - Yuanhuai Han
- Shanxi Agricultural University, Taigu, Shanxi, China
| | - Feng Yuan
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Linyi Zhang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Shuzhong Peng
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Erhu Guo
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
- * E-mail: (JW); (EG)
| |
Collapse
|
25
|
|
26
|
The Effect of Photoperiod on Flowering Time, Plant Architecture, and Biomass in Setaria. GENETICS AND GENOMICS OF SETARIA 2017. [DOI: 10.1007/978-3-319-45105-3_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
27
|
Doust AN, Mauro-Herrera M, Hodge JG, Stromski J. The C 4 Model Grass Setaria Is a Short Day Plant with Secondary Long Day Genetic Regulation. FRONTIERS IN PLANT SCIENCE 2017; 8:1062. [PMID: 28729868 PMCID: PMC5498473 DOI: 10.3389/fpls.2017.01062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 06/01/2017] [Indexed: 05/04/2023]
Abstract
The effect of photoperiod (day:night ratio) on flowering time was investigated in the wild species, Setaria viridis, and in a set of recombinant inbred lines (RILs) derived from a cross between foxtail millet (S. italica) and its wild ancestor green foxtail (S. viridis). Photoperiods totaled 24 h, with three trials of 8:16, 12:12 and 16:8 light:dark hour regimes for the RIL population, and these plus 10:14 and 14:10 for the experiments with S. viridis alone. The response of S. viridis to light intensity as well as photoperiod was assessed by duplicating photoperiods at two light intensities (300 and 600 μmol.m-2.s-1). In general, day lengths longer than 12 h delayed flowering time, although flowering time was also delayed in shorter day-lengths relative to the 12 h trial, even when daily flux in high intensity conditions exceeded that of the low intensity 12 h trial. Cluster analysis showed that the effect of photoperiod on flowering time differed between sets of RILs, with some being almost photoperiod insensitive and others being delayed with respect to the population as a whole in either short (8 or 12 h light) or long (16 h light) photoperiods. QTL results reveal a similar picture, with several major QTL colocalizing between the 8 and 12 h light trials, but with a partially different set of QTL identified in the 16 h trial. Major candidate genes for these QTL include several members of the PEBP protein family that includes Flowering Locus T (FT) homologs such as OsHd3a, OsRFT1, and ZCN8/12. Thus, Setaria is a short day plant (flowering quickest in short day conditions) whose flowering is delayed by long day lengths in a manner consistent with the responses of most other members of the grass family. However, the QTL results suggest that flowering time under long day conditions uses additional genetic pathways to those used under short day conditions.
Collapse
|
28
|
Grabowski PP, Evans J, Daum C, Deshpande S, Barry KW, Kennedy M, Ramstein G, Kaeppler SM, Buell CR, Jiang Y, Casler MD. Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data. THE NEW PHYTOLOGIST 2017; 213:154-169. [PMID: 27443672 DOI: 10.1111/nph.14101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/10/2016] [Indexed: 05/20/2023]
Abstract
Flowering time is a major determinant of biomass yield in switchgrass (Panicum virgatum), a perennial bioenergy crop, because later flowering allows for an extended period of vegetative growth and increased biomass production. A better understanding of the genetic regulation of flowering time in switchgrass will aid the development of switchgrass varieties with increased biomass yields, particularly at northern latitudes, where late-flowering but southern-adapted varieties have high winter mortality. We use genotypes derived from recently published exome-capture sequencing, which mitigates challenges related to the large, highly repetitive and polyploid switchgrass genome, to perform genome-wide association studies (GWAS) using flowering time data from a switchgrass association panel in an effort to characterize the genetic architecture and genes underlying flowering time regulation in switchgrass. We identify associations with flowering time at multiple loci, including in a homolog of FLOWERING LOCUS T and in a locus containing TIMELESS, a homolog of a key circadian regulator in animals. Our results suggest that flowering time variation in switchgrass is due to variation at many positions across the genome. The relationship of flowering time and geographic origin indicates likely roles for genes in the photoperiod and autonomous pathways in generating switchgrass flowering time variation.
Collapse
Affiliation(s)
- Paul P Grabowski
- US Dairy Forage Research Center, USDA-ARS, 1925 Linden Dr. W, Madison, WI, 53706, USA
| | - Joseph Evans
- DuPont Pioneer, Johnston, IA, 50131, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Kerrie W Barry
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Megan Kennedy
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Guillaume Ramstein
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr, Madison, WI, 53706, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Michael D Casler
- US Dairy Forage Research Center, USDA-ARS, 1925 Linden Dr. W, Madison, WI, 53706, USA
| |
Collapse
|
29
|
Acharya BR, Roy Choudhury S, Estelle AB, Vijayakumar A, Zhu C, Hovis L, Pandey S. Optimization of Phenotyping Assays for the Model Monocot Setaria viridis. FRONTIERS IN PLANT SCIENCE 2017; 8:2172. [PMID: 29312412 PMCID: PMC5743732 DOI: 10.3389/fpls.2017.02172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/11/2017] [Indexed: 05/02/2023]
Abstract
Setaria viridis (green foxtail) is an important model plant for the study of C4 photosynthesis in panicoid grasses, and is fast emerging as a system of choice for the study of plant development, domestication, abiotic stress responses and evolution. Basic research findings in Setaria are expected to advance research not only in this species and its close relative S. italica (foxtail millet), but also in other panicoid grasses, many of which are important food or bioenergy crops. Here we report on the standardization of multiple growth and development assays for S. viridis under controlled conditions, and in response to several phytohormones and abiotic stresses. We optimized these assays at three different stages of the plant's life: seed germination and post-germination growth using agar plate-based assays, early seedling growth and development using germination pouch-based assays, and adult plant growth and development under environmentally controlled growth chambers and greenhouses. These assays will be useful for the community to perform large scale phenotyping analyses, mutant screens, comparative physiological analysis, and functional characterization of novel genes of Setaria or other related agricultural crops. Precise description of various growth conditions, effective treatment conditions and description of the resultant phenotypes will help expand the use of S. viridis as an effective model system.
Collapse
|
30
|
|
31
|
Pant SR, Irigoyen S, Doust AN, Scholthof KBG, Mandadi KK. Setaria: A Food Crop and Translational Research Model for C 4 Grasses. FRONTIERS IN PLANT SCIENCE 2016; 7:1885. [PMID: 28018413 PMCID: PMC5156725 DOI: 10.3389/fpls.2016.01885] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/29/2016] [Indexed: 05/23/2023]
Affiliation(s)
- Shankar R. Pant
- Texas A&M AgriLife Research and Extension Center, Texas A&M University SystemWeslaco, TX, USA
| | - Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Texas A&M University SystemWeslaco, TX, USA
| | - Andrew N. Doust
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State UniversityStillwater, OK, USA
| | - Karen-Beth G. Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M UniversityCollege Station, TX, USA
| | - Kranthi K. Mandadi
- Texas A&M AgriLife Research and Extension Center, Texas A&M University SystemWeslaco, TX, USA
- Department of Plant Pathology and Microbiology, Texas A&M UniversityCollege Station, TX, USA
| |
Collapse
|
32
|
Tsai KJ, Lu MYJ, Yang KJ, Li M, Teng Y, Chen S, Ku MSB, Li WH. Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance. Sci Rep 2016; 6:35076. [PMID: 27734962 PMCID: PMC5062080 DOI: 10.1038/srep35076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/23/2016] [Indexed: 12/23/2022] Open
Abstract
The diploid C4 plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains.
Collapse
Affiliation(s)
- Kevin J. Tsai
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 11574 Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 11221 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Kai-Jung Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Mengyun Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Yuchuan Teng
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Shihmay Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Maurice S. B. Ku
- Department of Bioagricultural Science, National Chiayi University, Chiayi, 60004 Taiwan
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
| |
Collapse
|
33
|
Fang X, Dong K, Wang X, Liu T, He J, Ren R, Zhang L, Liu R, Liu X, Li M, Huang M, Zhang Z, Yang T. A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv]. BMC Genomics 2016; 17:336. [PMID: 27146360 PMCID: PMC4857278 DOI: 10.1186/s12864-016-2628-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 04/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundation for marker-assisted selection for agronomic traits and yield improvement. RESULT A total of 10598 SSR markers were developed according to the reference genome sequence of foxtail millet cultivar 'Yugu1'. A total of 1013 SSR markers showing polymorphism between Yugu1 and Longgu7 were used to genotype 167 individuals from a Yugu1 × Longgu7 F2 population, and a high density genetic map was constructed. The genetic map contained 1035 loci and spanned 1318.8 cM with an average distance of 1.27 cM between adjacent markers. Based on agronomic and yield traits identified in 2 years, 29 QTL were identified for 11 traits with combined analysis and single environment analysis. These QTL explained from 7.0 to 14.3 % of phenotypic variation. Favorable QTL alleles for peduncle length originated from Longgu7 whereas favorable alleles for the other traits originated from Yugu1 except for qLMS6.1. CONCLUSIONS New SSR markers, a high density genetic map and QTL identified for agronomic and yield traits lay the ground work for functional gene mapping, map-based cloning and marker-assisted selection in foxtail millet.
Collapse
Affiliation(s)
- Xiaomei Fang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China
| | - Kongjun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China
| | - Xiaoqin Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China
| | - Tianpeng Liu
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China
| | - Jihong He
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China
| | - Ruiyu Ren
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China
| | - Lei Zhang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China
| | - Rui Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China
| | - Xueying Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China
| | - Man Li
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China
| | - Mengzhu Huang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China
| | - Zhengsheng Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, People's Republic of China.
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, People's Republic of China.
| |
Collapse
|
34
|
Mauro-Herrera M, Doust AN. Development and Genetic Control of Plant Architecture and Biomass in the Panicoid Grass, Setaria. PLoS One 2016; 11:e0151346. [PMID: 26985990 PMCID: PMC4795695 DOI: 10.1371/journal.pone.0151346] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/05/2016] [Indexed: 01/12/2023] Open
Abstract
The architecture of a plant affects its ability to compete for light and to respond to environmental stresses, thus affecting overall fitness and productivity. Two components of architecture, branching and height, were studied in 182 F7 recombinant inbred lines (RILs) at the vegetative, flowering and mature developmental stages in the panicoid C4 model grass system, Setaria. The RIL population was derived from a cross between domesticated S. italica (foxtail millet) and its wild relative S. viridis (green foxtail). In both field and greenhouse trials the wild parent was taller initially, started branching earlier, and flowered earlier, while the domesticated parent was shorter initially, but flowered later, producing a robust tall plant architecture with more nodes and leaves on the main culm and few or no branches. Biomass was highly correlated with height of the plant and number of nodes on the main culm, and generally showed a negative relationship with branch number. However, several of the RILs with the highest biomass in both trials were significantly more branched than the domesticated parent of the cross. Quantitative trait loci (QTL) analyses indicate that both height and branching are controlled by multiple genetic regions, often with QTL for both traits colocalizing in the same genomic regions. Genomic positions of several QTL colocalize with QTL in syntenic regions in other species and contain genes known to control branching and height in sorghum, maize, and switchgrass. Included in these is the ortholog of the rice SD-1 semi-dwarfing gene, which underlies one of the major Setaria height QTL. Understanding the relationships between height and branching patterns in Setaria, and their genetic control, is an important step to gaining a comprehensive knowledge of the development and genetic regulation of panicoid grass architecture.
Collapse
Affiliation(s)
- Margarita Mauro-Herrera
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Andrew N. Doust
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK 74078, United States of America
| |
Collapse
|
35
|
Huang P, Shyu C, Coelho CP, Cao Y, Brutnell TP. Setaria viridis as a Model System to Advance Millet Genetics and Genomics. FRONTIERS IN PLANT SCIENCE 2016; 7:1781. [PMID: 27965689 PMCID: PMC5124564 DOI: 10.3389/fpls.2016.01781] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/11/2016] [Indexed: 05/18/2023]
Abstract
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.
Collapse
|
36
|
Ermawar RA, Collins HM, Byrt CS, Henderson M, O'Donovan LA, Shirley NJ, Schwerdt JG, Lahnstein J, Fincher GB, Burton RA. Genetics and physiology of cell wall polysaccharides in the model C4 grass, Setaria viridis spp. BMC PLANT BIOLOGY 2015; 15:236. [PMID: 26432387 PMCID: PMC4592572 DOI: 10.1186/s12870-015-0624-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/21/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Setaria viridis has emerged as a model species for the larger C4 grasses. Here the cellulose synthase (CesA) superfamily has been defined, with an emphasis on the amounts and distribution of (1,3;1,4)-β-glucan, a cell wall polysaccharide that is characteristic of the grasses and is of considerable value for human health. METHODS Orthologous relationship of the CesA and Poales-specific cellulose synthase-like (Csl) genes among Setaria italica (Si), Sorghum bicolor (Sb), Oryza sativa (Os), Brachypodium distachyon (Bradi) and Hordeum vulgare (Hv) were compared using bioinformatics analysis. Transcription profiling of Csl gene families, which are involved in (1,3;1,4)-β-glucan synthesis, was performed using real-time quantitative PCR (Q-PCR). The amount of (1,3;1,4)-β-glucan was measured using a modified Megazyme assay. The fine structures of the (1,3;1,4)-β-glucan, as denoted by the ratio of cellotriosyl to cellotetraosyl residues (DP3:DP4 ratio) was assessed by chromatography (HPLC and HPAEC-PAD). The distribution and deposition of the MLG was examined using the specific antibody BG-1 and captured using fluorescence and transmission electron microscopy (TEM). RESULTS The cellulose synthase gene superfamily contains 13 CesA and 35 Csl genes in Setaria. Transcript profiling of CslF, CslH and CslJ gene families across a vegetative tissue series indicated that SvCslF6 transcripts were the most abundant relative to all other Csl transcripts. The amounts of (1,3;1,4)-β-glucan in Setaria vegetative tissues ranged from 0.2% to 2.9% w/w with much smaller amounts in developing grain (0.003% to 0.013% w/w). In general, the amount of (1,3;1,4)-β-glucan was greater in younger than in older tissues. The DP3:DP4 ratios varied between tissue types and across developmental stages, and ranged from 2.4 to 3.0:1. The DP3:DP4 ratios in developing grain ranged from 2.5 to 2.8:1. Micrographs revealing the distribution of (1,3;1,4)-β-glucan in walls of different cell types and the data were consistent with the quantitative (1,3;1,4)-β-glucan assays. CONCLUSION The characteristics of the cellulose synthase gene superfamily and the accumulation and distribution of (1,3;1,4)-β-glucans in Setaria are similar to those in other C4 grasses, including sorghum. This suggests that Setaria is a suitable model plant for cell wall polysaccharide biology in C4 grasses.
Collapse
Affiliation(s)
- Riksfardini A Ermawar
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - Helen M Collins
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - Caitlin S Byrt
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - Marilyn Henderson
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - Lisa A O'Donovan
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - Neil J Shirley
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - Julian G Schwerdt
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - Jelle Lahnstein
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - Geoffrey B Fincher
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - Rachel A Burton
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| |
Collapse
|
37
|
Liu H, Liu H, Zhou L, Zhang Z, Zhang X, Wang M, Li H, Lin Z. Parallel Domestication of the Heading Date 1 Gene in Cereals. Mol Biol Evol 2015; 32:2726-37. [PMID: 26116860 DOI: 10.1093/molbev/msv148] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of ecological environments during domestication, it is yet to be determined whether they have a common genetic basis for flowering time. In this study, we show, through map-based cloning, that flowering time in sorghum is controlled by a major quantitative trait locus (QTL) Heading Date 1 (HD1), located on chromosome 10. The causal gene encodes the CONSTANS gene family which contains a CCT domain. A 5-bp deletion of a minor allele present in the coding sequence leads to a gene frameshift that delays flowering in sorghum. In contrast, in foxtail millet, association mapping of HD1 showed a common causal site with a splicing variant from "GT" to "AT" that was highly correlated with flowering time. In addition, the rice HD1 gene is known to harbor several causal variants controlling flowering time. These data indicate that the major flowering time QTL HD1 was under parallel domestication in sorghum, foxtail millet, and rice. The pattern of common mixed minor, or even rare, causal alleles in HD1 across different species may be representative of the genetic basis of the domestication syndrome. Furthermore, large DNA sequence analysis of HD1 revealed multiple origins for domesticated sorghum and a single origin for domesticated foxtail millet.
Collapse
Affiliation(s)
- Huanhuan Liu
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, China
| | - Hangqin Liu
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, China
| | - Leina Zhou
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, China
| | - Zhihai Zhang
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, China
| | - Xuan Zhang
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, China
| | - Mingli Wang
- Plant Genetic Resources Conservation Unit, USDA-ARS, Griffin, GA
| | - Haixia Li
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, China
| | - Zhongwei Lin
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, China
| |
Collapse
|
38
|
Jia G, Liu X, Schnable JC, Niu Z, Wang C, Li Y, Wang S, Wang S, Liu J, Guo E, Zhi H, Diao X. Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China. PLoS One 2015; 10:e0125688. [PMID: 25932649 PMCID: PMC4416935 DOI: 10.1371/journal.pone.0125688] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/24/2015] [Indexed: 11/18/2022] Open
Abstract
Crop improvement is a multifaceted micro-evolutionary process, involving changes in breeding approaches, planting configurations and consumption preferences of human beings. Recent research has started to identify the specific genes or genomic regions correlate to improved agronomic traits, however, an apparent blank between the genetic structure of crop elite varieties and their improving histories in diverse modern breeding programs is still in existence. Foxtail millet (Setaria italica) was one of the earliest cereal crops to be domesticated and served as a staple crop for early civilizations in China, where it is still widely grown today. In the present trial, a panel of foxtail millet elite varieties, which were released in the last sixty years in different geographical regions of China, was characterized using microsatellite markers (SSRs). A clear separation of two subpopulations corresponding to the two eco-geographical regions of foxtail millet production in China was identified by the dataset, which also indicated that in more recently released elite varieties, large quantities of accessions have been transferred from spring-sowing to summer-sowing ecotypes, likely as a result of breeding response to planting configurations. An association mapping study was conducted to identify loci controlling traits of major agronomic interest. Furthermore, selective sweeps involved in improvement of foxtail millet were identified as multi-diverse minor effect loci controlling different agronomic traits during the long-term improvement of elite varieties. Our results highlight the effect of transition of planting configuration and breeding preference on genetic evolvement of crop species.
Collapse
Affiliation(s)
- Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xiaotong Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - James C. Schnable
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Zhengang Niu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Chunfang Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yuhui Li
- Institute of Millet Crops, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, P. R. China
| | - Shujun Wang
- Institute of Millet Crops, Anyang Academy of Agricultural Sciences, Anyang, Henan, P. R. China
| | - Suying Wang
- Institute of Millet Crops, Anyang Academy of Agricultural Sciences, Anyang, Henan, P. R. China
| | - Jinrong Liu
- Institute of Millet Crops, Anyang Academy of Agricultural Sciences, Anyang, Henan, P. R. China
| | - Erhu Guo
- Institute of Millet Crops, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, P. R. China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| |
Collapse
|
39
|
Wang X, Bennetzen JL. Current status and prospects for the study of Nicotiana genomics, genetics, and nicotine biosynthesis genes. Mol Genet Genomics 2015; 290:11-21. [PMID: 25582664 DOI: 10.1007/s00438-015-0989-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 01/05/2015] [Indexed: 12/31/2022]
Abstract
Nicotiana, a member of the Solanaceae family, is one of the most important research model plants, and of high agricultural and economic value worldwide. To better understand the substantial and rapid research progress with Nicotiana in recent years, its genomics, genetics, and nicotine gene studies are summarized, with useful web links. Several important genetic maps, including a high-density map of N. tabacum consisting of ~2,000 markers published in 2012, provide tools for genetics research. Four whole genome sequences are from allotetraploid species, including N. benthamiana in 2012, and three N. tabacum cultivars (TN90, K326, and BX) in 2014. Three whole genome sequences are from diploids, including progenitors N. sylvestris and N. tomentosiformis in 2013 and N. otophora in 2014. These and additional studies provide numerous insights into genome evolution after polyploidization, including changes in gene composition and transcriptome expression in N. tabacum. The major genes involved in the nicotine biosynthetic pathway have been identified and the genetic basis of the differences in nicotine levels among Nicotiana species has been revealed. In addition, other progress on chloroplast, mitochondrial, and NCBI-registered projects on Nicotiana are discussed. The challenges and prospects for genomic, genetic and application research are addressed. Hence, this review provides important resources and guidance for current and future research and application in Nicotiana.
Collapse
Affiliation(s)
- Xuewen Wang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, People's Republic of China,
| | | |
Collapse
|
40
|
Muthamilarasan M, Prasad M. Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015. [PMID: 25239219 DOI: 10.1007/s00122-014-2399-325239219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent advances in Setaria genomics appear promising for genetic improvement of cereals and biofuel crops towards providing multiple securities to the steadily increasing global population. The prominent attributes of foxtail millet (Setaria italica, cultivated) and green foxtail (S. viridis, wild) including small genome size, short life-cycle, in-breeding nature, genetic close-relatedness to several cereals, millets and bioenergy grasses, and potential abiotic stress tolerance have accentuated these two Setaria species as novel model system for studying C4 photosynthesis, stress biology and biofuel traits. Considering this, studies have been performed on structural and functional genomics of these plants to develop genetic and genomic resources, and to delineate the physiology and molecular biology of stress tolerance, for the improvement of millets, cereals and bioenergy grasses. The release of foxtail millet genome sequence has provided a new dimension to Setaria genomics, resulting in large-scale development of genetic and genomic tools, construction of informative databases, and genome-wide association and functional genomic studies. In this context, this review discusses the advancements made in Setaria genomics, which have generated a considerable knowledge that could be used for the improvement of millets, cereals and biofuel crops. Further, this review also shows the nutritional potential of foxtail millet in providing health benefits to global population and provides a preliminary information on introgressing the nutritional properties in graminaceous species through molecular breeding and transgene-based approaches.
Collapse
Affiliation(s)
- Mehanathan Muthamilarasan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110 067, India
| | | |
Collapse
|
41
|
Muthamilarasan M, Prasad M. Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1-14. [PMID: 25239219 DOI: 10.1007/s00122-014-2399-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/11/2014] [Indexed: 05/18/2023]
Abstract
Recent advances in Setaria genomics appear promising for genetic improvement of cereals and biofuel crops towards providing multiple securities to the steadily increasing global population. The prominent attributes of foxtail millet (Setaria italica, cultivated) and green foxtail (S. viridis, wild) including small genome size, short life-cycle, in-breeding nature, genetic close-relatedness to several cereals, millets and bioenergy grasses, and potential abiotic stress tolerance have accentuated these two Setaria species as novel model system for studying C4 photosynthesis, stress biology and biofuel traits. Considering this, studies have been performed on structural and functional genomics of these plants to develop genetic and genomic resources, and to delineate the physiology and molecular biology of stress tolerance, for the improvement of millets, cereals and bioenergy grasses. The release of foxtail millet genome sequence has provided a new dimension to Setaria genomics, resulting in large-scale development of genetic and genomic tools, construction of informative databases, and genome-wide association and functional genomic studies. In this context, this review discusses the advancements made in Setaria genomics, which have generated a considerable knowledge that could be used for the improvement of millets, cereals and biofuel crops. Further, this review also shows the nutritional potential of foxtail millet in providing health benefits to global population and provides a preliminary information on introgressing the nutritional properties in graminaceous species through molecular breeding and transgene-based approaches.
Collapse
Affiliation(s)
- Mehanathan Muthamilarasan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110 067, India
| | | |
Collapse
|
42
|
Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, Chapman JA, Rokhsar DS, Schmutz J, Juenger TE. The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. THE NEW PHYTOLOGIST 2015; 205:402-14. [PMID: 25252269 PMCID: PMC4265272 DOI: 10.1111/nph.13027] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 07/31/2014] [Indexed: 05/08/2023]
Abstract
The process of plant speciation often involves the evolution of divergent ecotypes in response to differences in soil water availability between habitats. While the same set of traits is frequently associated with xeric/mesic ecotype divergence, it is unknown whether those traits evolve independently or if they evolve in tandem as a result of genetic colocalization either by pleiotropy or genetic linkage. The self-fertilizing C4 grass species Panicum hallii includes two major ecotypes found in xeric (var. hallii) or mesic (var. filipes) habitats. We constructed the first linkage map for P. hallii by genotyping a reduced representation genomic library of an F2 population derived from an intercross of var. hallii and filipes. We then evaluated the genetic architecture of divergence between these ecotypes through quantitative trait locus (QTL) mapping. Overall, we mapped QTLs for nine morphological traits that are involved in the divergence between the ecotypes. QTLs for five key ecotype-differentiating traits all colocalized to the same region of linkage group five. Leaf physiological traits were less divergent between ecotypes, but we still mapped five physiological QTLs. We also discovered a two-locus Dobzhansky-Muller hybrid incompatibility. Our study suggests that ecotype-differentiating traits may evolve in tandem as a result of genetic colocalization.
Collapse
Affiliation(s)
- David B Lowry
- Department of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA; Division of Science and Environmental Policy, California State University, Monterey Bay, 100 Campus Center, Seaside, CA, 93955, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
Maize occupies dual roles as both (a) one of the big-three grain species (along with rice and wheat) responsible for providing more than half of the calories consumed around the world, and (b) a model system for plant genetics and cytogenetics dating back to the origin of the field of genetics in the early twentieth century. The long history of genetic investigation in this species combined with modern genomic and quantitative genetic data has provided particular insight into the characteristics of genes linked to phenotypes and how these genes differ from many other sequences in plant genomes that are not easily distinguishable based on molecular data alone. These recent results suggest that the number of genes in plants that make significant contributions to phenotype may be lower than the number of genes defined by current molecular criteria, and also indicate that syntenic conservation has been underemphasized as a marker for gene function.
Collapse
Affiliation(s)
- James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583;
| |
Collapse
|
44
|
Qie L, Jia G, Zhang W, Schnable J, Shang Z, Li W, Liu B, Li M, Chai Y, Zhi H, Diao X. Mapping of quantitative trait locus (QTLs) that contribute to germination and early seedling drought tolerance in the interspecific cross Setaria italica×Setaria viridis. PLoS One 2014; 9:e101868. [PMID: 25033201 PMCID: PMC4102488 DOI: 10.1371/journal.pone.0101868] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 06/12/2014] [Indexed: 12/25/2022] Open
Abstract
Drought tolerance is an important breeding target for enhancing the yields of grain crop species in arid and semi-arid regions of the world. Two species of Setaria, domesticated foxtail millet (S. italica) and its wild ancestor green foxtail (S. viridis) are becoming widely adopted as models for functional genomics studies in the Panicoid grasses. In this study, the genomic regions controlling germination and early seedling drought tolerance in Setaria were identified using 190 F7 lines derived from a cross between Yugu1, a S. italica cultivar developed in China, and a wild S. viridis genotype collected from Uzbekistan. Quantitative trait loci were identified which contribute to a number of traits including promptness index, radical root length, coleoptile length and lateral root number at germinating stage and seedling survival rate was characterized by the ability of desiccated seedlings to revive after rehydration. A genetic map with 128 SSR markers which spans 1293.9 cM with an average of 14 markers per linkage group of the 9 linkage groups was constructed. A total of eighteen QTLs were detected which included nine that explained over 10% of the phenotypic variance for a given trait. Both the wild green foxtail genotype and the foxtail millet cultivar contributed the favorite alleles for traits detected in this trial, indicating that wild Setaria viridis populations may serve as a reservoir for novel stress tolerance alleles which could be employed in foxtail millet breeding.
Collapse
Affiliation(s)
- Lufeng Qie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenying Zhang
- Institute of Dry Land Agriculture, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - James Schnable
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonglin Shang
- College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Wei Li
- Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Binhui Liu
- Institute of Dry Land Agriculture, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Mingzhe Li
- Institute of Dry Land Agriculture, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Yang Chai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (XD); (HZ)
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- * E-mail: (XD); (HZ)
| |
Collapse
|
45
|
Warnasooriya SN, Brutnell TP. Enhancing the productivity of grasses under high-density planting by engineering light responses: from model systems to feedstocks. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2825-34. [PMID: 24868036 DOI: 10.1093/jxb/eru221] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The successful commercialization of bioenergy grasses as lignocellulosic feedstocks requires that they be produced, processed, and transported efficiently. Intensive breeding for higher yields in food crops has resulted in varieties that perform optimally under high-density planting but often with high input costs. This is particularly true of maize, where most yield gains in the past have come through increased planting densities and an abundance of fertilizer. For lignocellulosic feedstocks, biomass rather than grain yield and digestibility of cell walls are two of the major targets for improvement. Breeding for high-density performance of lignocellulosic crops has been much less intense and thus provides an opportunity for improving the feedstock potential of these grasses. In this review, we discuss the role of vegetative shade on growth and development and suggest targets for manipulating this response to increase harvestable biomass under high-density planting. To engineer grass architecture and modify biomass properties at increasing planting densities, we argue that new model systems are needed and recommend Setaria viridis, a panicoid grass, closely related to major fuel and bioenergy grasses as a model genetic system.
Collapse
|
46
|
Gupta S, Kumari K, Muthamilarasan M, Parida SK, Prasad M. Population structure and association mapping of yield contributing agronomic traits in foxtail millet. PLANT CELL REPORTS 2014; 33:881-93. [PMID: 24413764 DOI: 10.1007/s00299-014-1564-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 12/06/2013] [Accepted: 12/31/2013] [Indexed: 05/20/2023]
Abstract
Association analyses accounting for population structure and relative kinship identified eight SSR markers ( p < 0.01) showing significant association ( R (2) = 18 %) with nine agronomic traits in foxtail millet. Association mapping is an efficient tool for identifying genes regulating complex traits. Although association mapping using genomic simple sequence repeat (SSR) markers has been successfully demonstrated in many agronomically important crops, very few reports are available on marker-trait association analysis in foxtail millet. In the present study, 184 foxtail millet accessions from diverse geographical locations were genotyped using 50 SSR markers representing the nine chromosomes of foxtail millet. The genetic diversity within these accessions was examined using a genetic distance-based and a general model-based clustering method. The model-based analysis using 50 SSR markers identified an underlying population structure comprising five sub-populations which corresponded well with distance-based groupings. The phenotyping of plants was carried out in the field for three consecutive years for 20 yield contributing agronomic traits. The linkage disequilibrium analysis considering population structure and relative kinship identified eight SSR markers (p < 0.01) on different chromosomes showing significant association (R (2) = 18 %) with nine agronomic traits. Four of these markers were associated with multiple traits. The integration of genetic and physical map information of eight SSR markers with their functional annotation revealed strong association of two markers encoding for phospholipid acyltransferase and ubiquitin carboxyl-terminal hydrolase located on the same chromosome (5) with flag leaf width and grain yield, respectively. Our findings on association mapping is the first report on Indian foxtail millet germplasm and this could be effectively applied in foxtail millet breeding to further uncover marker-trait associations with a large number of markers.
Collapse
Affiliation(s)
- Sarika Gupta
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110 067, India
| | | | | | | | | |
Collapse
|
47
|
Doust AN, Lukens L, Olsen KM, Mauro-Herrera M, Meyer A, Rogers K. Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication. Proc Natl Acad Sci U S A 2014; 111:6178-83. [PMID: 24753598 PMCID: PMC4035984 DOI: 10.1073/pnas.1308940110] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Domestication is a multifaceted evolutionary process, involving changes in individual genes, genetic interactions, and emergent phenotypes. There has been extensive discussion of the phenotypic characteristics of plant domestication, and recent research has started to identify the specific genes and mutational mechanisms that control domestication traits. However, there is an apparent disconnect between the simple genetic architecture described for many crop domestication traits, which should facilitate rapid phenotypic change under selection, and the slow rate of change reported from the archeobotanical record. A possible explanation involves the middle ground between individual genetic changes and their expression during development, where gene-by-gene (epistatic) and gene-by-environment interactions can modify the expression of phenotypes and opportunities for selection. These aspects of genetic architecture have the potential to significantly slow the speed of phenotypic evolution during crop domestication and improvement. Here we examine whether epistatic and gene-by-environment interactions have shaped how domestication traits have evolved. We review available evidence from the literature, and we analyze two domestication-related traits, shattering and flowering time, in a mapping population derived from a cross between domesticated foxtail millet and its wild progenitor. We find that compared with wild progenitor alleles, those favored during domestication often have large phenotypic effects and are relatively insensitive to genetic background and environmental effects. Consistent selection should thus be able to rapidly change traits during domestication. We conclude that if phenotypic evolution was slow during crop domestication, this is more likely due to cultural or historical factors than epistatic or environmental constraints.
Collapse
Affiliation(s)
- Andrew N. Doust
- Botany Department, Oklahoma State University, Stillwater, OK 74078
| | - Lewis Lukens
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G2W1; and
| | - Kenneth M. Olsen
- Department of Biology, Washington University, St. Louis, MO 63130
| | | | - Ann Meyer
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G2W1; and
| | - Kimberly Rogers
- Botany Department, Oklahoma State University, Stillwater, OK 74078
| |
Collapse
|
48
|
Meyer RS, Purugganan MD. Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet 2014; 14:840-52. [PMID: 24240513 DOI: 10.1038/nrg3605] [Citation(s) in RCA: 582] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.
Collapse
Affiliation(s)
- Rachel S Meyer
- Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place, New York University, New York 10003, USA
| | | |
Collapse
|
49
|
Coelho CP, Minow MAA, Chalfun-Júnior A, Colasanti J. Putative sugarcane FT/TFL1 genes delay flowering time and alter reproductive architecture in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2014; 5:221. [PMID: 24904616 PMCID: PMC4033272 DOI: 10.3389/fpls.2014.00221] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/03/2014] [Indexed: 05/05/2023]
Abstract
Agriculturally important grasses such as rice, maize, and sugarcane are evolutionarily distant from Arabidopsis, yet some components of the floral induction process are highly conserved. Flowering in sugarcane is an important factor that negatively affects cane yield and reduces sugar/ethanol production from this important perennial bioenergy crop. Comparative studies have facilitated the identification and characterization of putative orthologs of key flowering time genes in sugarcane, a complex polyploid plant whose genome has yet to be sequenced completely. Using this approach we identified phosphatidylethanolamine-binding protein (PEBP) gene family members in sugarcane that are similar to the archetypical FT and TFL1 genes of Arabidopsis that play an essential role in controlling the transition from vegetative to reproductive growth. Expression analysis of ScTFL1, which falls into the TFL1-clade of floral repressors, showed transcripts in developing leaves surrounding the shoot apex but not at the apex itself. ScFT1 was detected in immature leaves and apical regions of vegetatively growing plants and, after the floral transition, expression also occurred in mature leaves. Ectopic over-expression of ScTFL1 in Arabidopsis caused delayed flowering in Arabidopsis, as might be expected for a gene related to TFL1. In addition, lines with the latest flowering phenotype exhibited aerial rosette formation. Unexpectedly, over-expression of ScFT1, which has greatest similarity to the florigen-encoding FT, also caused a delay in flowering. This preliminary analysis of divergent sugarcane FT and TFL1 gene family members from Saccharum spp. suggests that their expression patterns and roles in the floral transition has diverged from the predicted role of similar PEBP family members.
Collapse
Affiliation(s)
- Carla P. Coelho
- Setor de Fisiologia Vegetal, Departamento de Biologia, Universidade Federal de LavrasLavras, Brazil
- Department of Molecular and Cellular Biology, University of GuelphGuelph, ON, Canada
| | - Mark A. A. Minow
- Department of Molecular and Cellular Biology, University of GuelphGuelph, ON, Canada
| | - Antonio Chalfun-Júnior
- Setor de Fisiologia Vegetal, Departamento de Biologia, Universidade Federal de LavrasLavras, Brazil
| | - Joseph Colasanti
- Department of Molecular and Cellular Biology, University of GuelphGuelph, ON, Canada
- *Correspondence: Joseph Colasanti, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada e-mail:
| |
Collapse
|
50
|
Jia G, Shi S, Wang C, Niu Z, Chai Y, Zhi H, Diao X. Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3645-56. [PMID: 23956411 PMCID: PMC3745726 DOI: 10.1093/jxb/ert198] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Green foxtail (Setaria viridis) is a new model plant for the genomic investigation of C4 photosynthesis biology. As the ancestor of foxtail millet (Setaria italica), an ancient cereal of great importance in arid regions of the world, green foxtail is crucial for the study of domestication and evolution of this ancient crop. In the present study, 288 green foxtail accessions, which were collected from all geographical regions of China, were analysed using 77 simple sequence repeats (SSRs) that cover the whole genome. A high degree of molecular diversity was detected in these accessions, with an average of 33.5 alleles per locus. Two clusters, which were inconsistent with the distribution of eco-geographical regions in China, were inferred from STRUCTURE, Neighbor-Joining, and principal component analysis, indicating a partially mixed distribution of Chinese green foxtails. The higher subpopulation diversity was from accessions mainly collected from North China. A low level of linkage disequilibrium was observed in the green foxtail genome. Furthermore, a combined analysis of green foxtail and foxtail millet landraces was conducted, and the origin and domestication of foxtail millet was inferred in North China.
Collapse
Affiliation(s)
- Guanqing Jia
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, the Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Shenkui Shi
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, the Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Chunfang Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, the Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Zhengang Niu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, the Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Yang Chai
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, the Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Hui Zhi
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, the Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xianmin Diao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, the Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| |
Collapse
|