1
|
Hoque A, Fiedler JD, Rahman M. Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection. BMC Genomics 2020; 21:557. [PMID: 32795254 PMCID: PMC7430851 DOI: 10.1186/s12864-020-06922-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/17/2020] [Indexed: 11/25/2022] Open
Abstract
Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6200 SNP markers. Results All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r = 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest (Fst > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree and kinship matrix assist to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.
Collapse
Affiliation(s)
- Ahasanul Hoque
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Jason D Fiedler
- Cereal Crops Research, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, USA
| | - Mukhlesur Rahman
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
| |
Collapse
|
2
|
Zhang J, Qi Y, Wang L, Wang L, Yan X, Dang Z, Li W, Zhao W, Pei X, Li X, Liu M, Tan M, Wang L, Long Y, Wang J, Zhang X, Dang Z, Zheng H, Liu T. Genomic Comparison and Population Diversity Analysis Provide Insights into the Domestication and Improvement of Flax. iScience 2020; 23:100967. [PMID: 32240956 PMCID: PMC7114909 DOI: 10.1016/j.isci.2020.100967] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/17/2020] [Accepted: 03/03/2020] [Indexed: 01/23/2023] Open
Abstract
Flax has been cultivated for its oil and fiber for thousands of years. However, it remains unclear how the modifications of agronomic traits occurred on the genetic level during flax cultivation. In this study, we conducted genome-wide variation analyses on multiple accessions of oil-use, fiber-use, landraces, and pale flax to identify the genomic variations during flax cultivation. Our findings indicate that, during flax domestication, genes relevant to flowering, dehiscence, oil production, and plant architecture were preferentially selected. Furthermore, regardless of origins, the improvement of the modern oil-use flax preceded that of the fiber-use flax, although the dual selection on oil-use and fiber-use characteristics might have occurred in the early flax domestication. We also found that the expansion of MYB46/MYB83 genes may have contributed to the unique secondary cell wall biosynthesis in flax and the directional selections on MYB46/MYB83 may have shaped the morphological profile of the current oil-use and fiber-use flax. Assemblies of genomes, including oil-use flax, fiber-use flax and pale flax Comparative genomic analysis between pale flax and cultivated flax Dual-selection mode on oil-use and fiber-use characteristics might be existing Expansion and selection of MYB46/MYB83 may shape the morphological profile of flax
Collapse
Affiliation(s)
- Jianping Zhang
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China.
| | - Yanni Qi
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Limin Wang
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Lili Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Xingchu Yan
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Zhao Dang
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Wenjuan Li
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Wei Zhao
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xinwu Pei
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Meilian Tan
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Lei Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Xuewen Zhang
- Biomarker Technologies Corporation, Beijing, China
| | - Zhanhai Dang
- Institute of Crop Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China.
| | | | - Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, China.
| |
Collapse
|
3
|
Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production. Sci Rep 2019; 9:976. [PMID: 30700760 PMCID: PMC6354013 DOI: 10.1038/s41598-018-37086-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 11/02/2018] [Indexed: 01/30/2023] Open
Abstract
After domestication in the Near East around 10,000 years ago several founder crops, flax included, spread to European latitudes. On reaching northerly latitudes the architecture of domesticated flax became more suitable to fiber production over oil, with longer stems, smaller seeds and fewer axillary branches. Latitudinal adaptations in crops typically result in changes in flowering time, often involving the PEBP family of genes that also have the potential to influence plant architecture. Two PEBP family genes in the flax genome, LuTFL1 and LuTFL2, vary in wild and cultivated flax over latitudinal range with cultivated flax receiving LuTFL1 alleles from northerly wild flax populations. Compared to a background of population structure of flaxes over latitude, the LuTFL1 alleles display a level of differentiation that is consistent with selection for an allele III in the north. We demonstrate through heterologous expression in Arabidopsis thaliana that LuTFL1 is a functional homolog of TFL1 in A. thaliana capable of changing both flowering time and plant architecture. We conclude that specialized fiber flax types could have formed as a consequence of a natural adaptation of cultivated flax to higher latitudes.
Collapse
|
4
|
He L, Xiao J, Rashid KY, Yao Z, Li P, Jia G, Wang X, Cloutier S, You FM. Genome-Wide Association Studies for Pasmo Resistance in Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2019; 9:1982. [PMID: 30693010 PMCID: PMC6339956 DOI: 10.3389/fpls.2018.01982] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/20/2018] [Indexed: 05/04/2023]
Abstract
Pasmo is one of the most widespread diseases threatening flax production. To identify genetic regions associated with pasmo resistance (PR), a genome-wide association study was performed on 370 accessions from the flax core collection. Evaluation of pasmo severity was performed in the field from 2012 to 2016 in Morden, MB, Canada. Genotyping-by-sequencing has identified 258,873 single nucleotide polymorphisms (SNPs) distributed on all 15 flax chromosomes. Marker-trait associations were identified using ten different statistical models. A total of 692 unique quantitative trait nucleotides (QTNs) associated with 500 putative quantitative trait loci (QTL) were detected from six phenotypic PR datasets (five individual years and average across years). Different QTNs were identified with various statistical models and from individual PR datasets, indicative of the complementation between analytical methods and/or genotype × environment interactions of the QTL effects. The single-locus models tended to identify large-effect QTNs while the multi-loci models were able to detect QTNs with smaller effects. Among the putative QTL, 67 had large effects (3-23%), were stable across all datasets and explained 32-64% of the total variation for PR in the various datasets. Forty-five of these QTL spanned 85 resistance gene analogs including a large toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (TNL) type gene cluster on chromosome 8. The number of QTL with positive-effect or favorite alleles (NPQTL) in accessions was significantly correlated with PR (R 2 = 0.55), suggesting that these QTL effects are mainly additive. NPQTL was also significantly associated with morphotype (R 2 = 0.52) and major QTL with positive effect alleles were present in the fiber type accessions. The 67 large effect QTL are suited for marker-assisted selection and the 500 QTL for effective genomic prediction in PR molecular breeding.
Collapse
Affiliation(s)
- Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - Jin Xiao
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - Khalid Y. Rashid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Pingchuan Li
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Gaofeng Jia
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Xiue Wang
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| |
Collapse
|
5
|
Rajwade AV, Joshi RS, Kadoo NY, Gupta VS. Sequence characterization and in silico structure prediction of fatty acid desaturases in linseed varieties with differential fatty acid composition. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:4896-4906. [PMID: 27109704 DOI: 10.1002/jsfa.7775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND Linseed is the richest agricultural source of α-linolenic acid (ALA), an ω-3 fatty acid (FA) that offers several nutritional benefits. In the present study, sequence characterization of six desaturase genes (SAD1, SAD2, FAD2, FAD2-2, FAD3A and FAD3B) and 3D structure prediction of their proteins from ten Indian linseed varieties differing in ALA content were performed to determine whether the nucleotide and amino acid (AA) sequence variants have any functional implications in differential accumulation of ALA or other FAs in linseed. RESULTS The SAD and FAD2 genes exhibited few sequence variations among the ten varieties, forming only one or two protein isoforms. In contrast, the FAD3A and FAD3B genes showed more sequence variations and three or four protein isoforms. Interestingly, the two high-ALA varieties NL260 and Padmini had the same FAD3B nucleotide and protein isoforms, which differed from all other varieties. Surprisingly, no AA changes altered the 3D structures of the desaturase proteins. CONCLUSION Several nucleotide and AA sequence variations in desaturase genes were observed; however, they did not alter the 3D structure of any desaturase protein and were not correlated with FA levels among the ten linseed varieties, which had different ALA contents. This suggests a complex regulatory process of biosynthesis of FAs in linseed. © 2016 Society of Chemical Industry.
Collapse
Affiliation(s)
- Ashwini V Rajwade
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India
| | - Rakesh S Joshi
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India
| | - Narendra Y Kadoo
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India.
| | - Vidya S Gupta
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India.
| |
Collapse
|
6
|
|
7
|
Fu YB. Population-based resequencing revealed an ancestral winter group of cultivated flax: implication for flax domestication processes. Ecol Evol 2012; 2:622-35. [PMID: 22822439 PMCID: PMC3399149 DOI: 10.1002/ece3.101] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 11/28/2011] [Accepted: 11/29/2011] [Indexed: 11/29/2022] Open
Abstract
Cultivated flax (Linum usitatissimum L.) is the earliest oil and fiber crop and its early domestication history may involve multiple events of domestication for oil, fiber, capsular indehiscence, and winter hardiness. Genetic studies have demonstrated that winter cultivated flax is closely related to oil and fiber cultivated flax and shows little relatedness to its progenitor, pale flax (L. bienne Mill.), but winter hardiness is one major characteristic of pale flax. Here, we assessed the genetic relationships of 48 Linum samples representing pale flax and four trait-specific groups of cultivated flax (dehiscent, fiber, oil, and winter) through population-based resequencing at 24 genomic regions, and revealed a winter group of cultivated flax that displayed close relatedness to the pale flax samples. Overall, the cultivated flax showed a 27% reduction of nucleotide diversity when compared with the pale flax. Recombination frequently occurred at these sampled genomic regions, but the signal of selection and bottleneck was relatively weak. These findings provide some insight into the impact and processes of flax domestication and are significant for expanding our knowledge about early flax domestication, particularly for winter hardiness.
Collapse
Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| |
Collapse
|