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Shi K, Dong H, Du H, Li Y, Zhou L, Liang C, Şakiroğlu M, Wang Z. The chromosome-level assembly of the wild diploid alfalfa genome provides insights into the full landscape of genomic variations between cultivated and wild alfalfa. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1757-1772. [PMID: 38288521 PMCID: PMC11123407 DOI: 10.1111/pbi.14300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 11/22/2023] [Accepted: 01/15/2024] [Indexed: 05/25/2024]
Abstract
Alfalfa (Medicago sativa L.) is one of the most important forage legumes in the world, including autotetraploid (M. sativa ssp. sativa) and diploid alfalfa (M. sativa ssp. caerulea, progenitor of autotetraploid alfalfa). Here, we reported a high-quality genome of ZW0012 (diploid alfalfa, 769 Mb, contig N50 = 5.5 Mb), which was grouped into the Northern group in population structure analysis, suggesting that our genome assembly filled a major gap among the members of M. sativa complex. During polyploidization, large phenotypic differences occurred between diploids and tetraploids, and the genetic information underlying its massive phenotypic variations remains largely unexplored. Extensive structural variations (SVs) were identified between ZW0012 and XinJiangDaYe (an autotetraploid alfalfa with released genome). We identified 71 ZW0012-specific PAV genes and 1296 XinJiangDaYe-specific PAV genes, mainly involved in defence response, cell growth, and photosynthesis. We have verified the positive roles of MsNCR1 (a XinJiangDaYe-specific PAV gene) in nodulation using an Agrobacterium rhizobia-mediated transgenic method. We also demonstrated that MsSKIP23_1 and MsFBL23_1 (two XinJiangDaYe-specific PAV genes) regulated leaf size by transient overexpression and virus-induced gene silencing analysis. Our study provides a high-quality reference genome of an important diploid alfalfa germplasm and a valuable resource of variation landscape between diploid and autotetraploid, which will facilitate the functional gene discovery and molecular-based breeding for the cultivars in the future.
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Affiliation(s)
- Kun Shi
- College of Grassland Science and TechnologycChina Agricultural UniversityBeijingChina
| | - Hongbin Dong
- College of Grassland Science and TechnologycChina Agricultural UniversityBeijingChina
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green DevelopmentHebei UniversityBaodingChina
| | - Yuxian Li
- School of Life SciencesNorth China University of Science and TechnologyTangshanChina
| | - Le Zhou
- College of Grassland Science and TechnologycChina Agricultural UniversityBeijingChina
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Muhammet Şakiroğlu
- Department of BioengineeringAdana AlparslanTürkeş Science and Technology UniversityAdanaTurkey
| | - Zan Wang
- College of Grassland Science and TechnologycChina Agricultural UniversityBeijingChina
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Rajpal VR, Raina SN, Rao SR, Sharma S, Choudhary A. Chromosome Complements and Karyological Studies in <i>Medicago</i> Species. CYTOLOGIA 2022. [DOI: 10.1508/cytologia.87.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University Sector 125
| | - Satyawada Rama Rao
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University
| | - Suman Sharma
- Department of Botany, Ramjas College, University of Delhi
| | - Amrita Choudhary
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University
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Shen C, Du H, Chen Z, Lu H, Zhu F, Chen H, Meng X, Liu Q, Liu P, Zheng L, Li X, Dong J, Liang C, Wang T. The Chromosome-Level Genome Sequence of the Autotetraploid Alfalfa and Resequencing of Core Germplasms Provide Genomic Resources for Alfalfa Research. MOLECULAR PLANT 2020; 13:1250-1261. [PMID: 32673760 DOI: 10.1016/j.molp.2020.07.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/24/2020] [Accepted: 07/10/2020] [Indexed: 05/20/2023]
Abstract
Alfalfa (Medicago sativa) is one of the most important forage crops in the world; however, its molecular genetics and breeding research are hindered due to the lack of a high-quality reference genome. Here, we report a de novo assembled 816-Mb high-quality, chromosome-level haploid genome sequence for 'Zhongmu No.1' alfalfa, a heterozygous autotetraploid. The contig N50 is 3.92 Mb, and 49 165 genes are annotated in the genome. The alfalfa genome is estimated to have diverged from M. truncatula approximately 8 million years ago. Genomic population analysis of 162 alfalfa accessions revealed high genetic diversity, weak population structure, and extensive gene flow from wild to cultivated alfalfa. Genome-wide association studies identified many candidate genes associated with important agronomic traits. Furthermore, we showed that MsFTa2, a Flowering Locus T homolog, whose expression is upregulated in salt-resistant germplasms, may be associated with fall dormancy and salt resistance. Taken together, these genomic resources will facilitate alfalfa genetic research and agronomic improvement.
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Affiliation(s)
- Chen Shen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhuo Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Hongwei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Fugui Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hong Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiangzhao Meng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qianwen Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Peng Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lihua Zheng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiuxiu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
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Franco AL, Figueredo A, Pereira LDM, de Sousa SM, Souza G, Carvalho MA, Simon MF, Viccini LF. Low cytomolecular diversification in the genus Stylosanthes Sw. (Papilionoideae, Leguminosae). Genet Mol Biol 2020; 43:e20180250. [PMID: 31429856 PMCID: PMC7197990 DOI: 10.1590/1678-4685-gmb-2018-0250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/07/2019] [Indexed: 12/02/2022] Open
Abstract
Stylosanthes (Papilionoideae, Leguminosae) is a predominantly Neotropical genus with ~48 species that include worldwide important forage species. This study presents the chromosome number and morphology of eight species of the genus Stylosanthes (S. acuminata, S. gracilis, S. grandifolia, S. guianensis, S. hippocampoides, S. pilosa, S. macrocephala, and S. ruellioides). In addition, staining with CMA and DAPI, in situ hybridization with 5S and 35S rDNA probes, and estimation of DNA content were performed. The interpretation of Stylosanthes chromosome diversification was anchored by a comparison with the sister genus Arachis and a dated molecular phylogeny based on nuclear and plastid loci. Stylosanthes species showed 2n = 20, with low cytomolecular diversification regarding 5S rDNA, 35S rDNA, and genome size. Arachis has a more ancient diversification (~7 Mya in the Pliocene) than the relatively recent Stylosanthes (~2 Mya in the Pleistocene), and it seems more diverse than its sister lineage. Our data support the idea that the cytomolecular stability of Stylosanthes in relation to Arachis could be a result of its recent origin. The recent diversification of Stylosanthes could also be related to the low morphological differentiation among species, and to the recurrent formation of allopolyploid complexes.
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Affiliation(s)
- Ana Luiza Franco
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
| | - Amanda Figueredo
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | - Lívia de Moraes Pereira
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | - Saulo Marçal de Sousa
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
| | - Gustavo Souza
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | | | - Marcelo F. Simon
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Recursos Genéticos e Biotecnologia, PqEB, Brasília, DF, Brazil
| | - Lyderson Facio Viccini
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
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Lei Y, Xu Y, Hettenhausen C, Lu C, Shen G, Zhang C, Li J, Song J, Lin H, Wu J. Comparative analysis of alfalfa (Medicago sativa L.) leaf transcriptomes reveals genotype-specific salt tolerance mechanisms. BMC PLANT BIOLOGY 2018; 18:35. [PMID: 29448940 PMCID: PMC5815232 DOI: 10.1186/s12870-018-1250-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/30/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Soil salinity is an important factor affecting growth, development, and productivity of almost all land plants, including the forage crop alfalfa (Medicago sativa). However, little is known about how alfalfa responds and adapts to salt stress, particularly among different salt-tolerant cultivars. RESULTS Among seven alfalfa cultivars, we found that Zhongmu-1 (ZM) is relatively salt-tolerant and Xingjiang Daye (XJ) is salt-sensitive. Compared to XJ, ZM showed slower growth under low-salt conditions, but exhibited stronger tolerance to salt stress. RNA-seq analysis revealed 2237 and 1125 differentially expressed genes (DEGs) between ZM and XJ in the presence and absence of salt stress, among which many genes are involved in stress-related pathways. After salt treatment, compared with the controls, the number of DEGs in XJ (19373) was about four times of that in ZM (4833). We also detected specific differential gene expression patterns: In response to salt stress, compared with XJ, ZM maintained relatively more stable expression levels of genes related to the ROS and Ca2+ pathways, phytohormone biosynthesis, and Na+/K+ transport. Notably, several salt resistance-associated genes always showed greater levels of expression in ZM than in XJ, including a transcription factor. Consistent with the suppression of plant growth resulting from salt stress, the expression of numerous photosynthesis- and growth hormone-related genes decreased more dramatically in XJ than in ZM. By contrast, the expression levels of photosynthetic genes were lower in ZM under low-salt conditions. CONCLUSIONS Compared with XJ, ZM is a salt-tolerant alfalfa cultivar possessing specific regulatory mechanisms conferring exceptional salt tolerance, likely by maintaining high transcript levels of abiotic and biotic stress resistance-related genes. Our results suggest that maintaining this specific physiological status and/or plant adaptation to salt stress most likely arises by inhibition of plant growth in ZM through plant hormone interactions. This study identifies new candidate genes that may regulate alfalfa tolerance to salt stress and increases the understanding of the genetic basis for salt tolerance.
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Affiliation(s)
- Yunting Lei
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610000 China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Yuxing Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Christian Hettenhausen
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Chengkai Lu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Guojing Shen
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Cuiping Zhang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Jing Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Juan Song
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Honghui Lin
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610000 China
| | - Jianqiang Wu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
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