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Yang J, Han J, Jing Y, Li S, Lan B, Zhang Q, Yin K. Virulent Fusarium isolates with diverse morphologies show similar invasion and colonization strategies in alfalfa. FRONTIERS IN PLANT SCIENCE 2024; 15:1390069. [PMID: 38828216 PMCID: PMC11140090 DOI: 10.3389/fpls.2024.1390069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/30/2024] [Indexed: 06/05/2024]
Abstract
Root rot is a major disease that causes decline of alfalfa production, and Fusarium is a major pathogen associated with root rot. In this study, 13 Fusarium isolates were obtained from alfalfa with root rot in Gansu Province, the major alfalfa production region in China. The isolates were characterized by molecular genotyping (ITS, TEF 1-α and RPB2 fragments) and identified as six species, which included the F. acuminatum, F. incarnatum, F. oxysporum, F. proliferatum, F. redolens, and F. solani. We found that their morphology varied significantly at both the macro- and micro-levels, even for those from the same species. We developed a low cost and fast pathogenicity test and revealed that all isolates were pathogenic to alfalfa with typical root rot symptoms such as leaf yellowing and brown lesions on the root and stem. However, the virulence of the isolates differed. We also found that the conidia of all isolates germinated as early as 24 hours post inoculation (hpi), while hyphae colonized the root extensively and invaded the xylem vessel by 48 hpi. Together our results reveal that different virulent Fusarium isolates use a similar invasion strategy in alfalfa. This natural plant-fungus pathosystem is intriguing and warrants further examination, particularly with regard to efforts aimed at mitigating the impact of multiple similar vascular pathogens on infected alfalfa plants.
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Affiliation(s)
- Jian Yang
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Jing Han
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Yuqing Jing
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Siyang Li
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Bo Lan
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Qian Zhang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Kangquan Yin
- School of Grassland Science, Beijing Forestry University, Beijing, China
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Du W, Huang H, Kong W, Jiang W, Pang Y. Over-expression of Medicago Acyl-CoA-binding 2 genes enhance salt and drought tolerance in Arabidopsis. Int J Biol Macromol 2024; 268:131631. [PMID: 38631584 DOI: 10.1016/j.ijbiomac.2024.131631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/11/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
Acyl-CoA-binding proteins (ACBPs) are mainly involved in acyl-CoA ester binding and trafficking in eukaryotic cells, and they function in lipid metabolism, membrane biosynthesis, cellular signaling, stress response, disease resistance, and other biological activities in plants. However, the roles of ACBP family members in Medicago remain unclear. In this study, a total of eight ACBP genes were identified in the genome of Medicago truncatula and Medicago sativa, and they were clustered into four sub-families (Class I-IV). Many cis-acting elements related to abiotic response were identified in the promoter region of these ACBP genes, in particular light-responsive elements. These ACBP genes exhibited distinct expression pattern in various tissues, and the expression level of MtACBP1/MsACBP1 and MtACBP2/MsACBP2 gene pairs were significantly increased under NaCl treatment. Subcellular localization analysis showed that MtACBP1/MsACBP1 and MtACBP2/MsACBP2 were localized in the endoplasmic reticulum of tobacco epidermal cells. Arabidopsis seedlings over-expressing MtACBP2/MsACBP2 displayed increased root length than the wild type under short light, Cu2+, ABA, PEG, and NaCl treatments. Over-expression of MtACBP2/MsACBP2 also significantly enhanced Arabidopsis tolerance under NaCl and PEG treatments in mature plants. Collectively, our study identified salt and drought responsive ACBP genes in Medicago and verified their functions in increasing resistance against salt and drought stresses.
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Affiliation(s)
- Wenxuan Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haijun Huang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weiye Kong
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenbo Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Zhang Y, Zhang Y, Wang C, Xiao J, Huang M, Zhuo L, Zhang D. Enhancement of salt tolerance of alfalfa: Physiological and molecular responses of transgenic alfalfa plants expressing Syntrichia caninervis-derived ScABI3. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108335. [PMID: 38190765 DOI: 10.1016/j.plaphy.2024.108335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Alfalfa (Medicago sativa L.), a perennial forage plant, is a rich source of nutrients such as vitamins, minerals, and proteins. Salt stress, however, impedes its growth. The plant-specific transcription factor abscisic acid insensitive 3 (ABI3) has a critical contribution to the control of abscisic acid (ABA) signaling pathway and abiotic stress response. The gene ScABI3 from Syntrichia caninervis, a moss species tolerant to desiccation, could be considered a potential candidate gene to modify alfalfa's nutritional and growth aspects. However, it remains unclear how ScABI3 affects the salt stress response of transgenic alfalfa. Therefore, we elucidated the role and molecular mechanism of ScABI3 from S. caninervis as an ABA signaling factor in transgenic alfalfa. Our findings demonstrate that ScABI3 overexpression in transgenic alfalfa improves salt tolerance by promoting relative water content, antioxidant enzyme activity, and photosynthetic parameters. Furthermore, the key genes of plant hormone signaling and the classical salt tolerance pathway were activated in ScABI3 transgenic lines under salt stress. Based on these results, ScABI3 could be considered a potentially critical candidate gene to alleviate salt stress in alfalfa. The present study provides valuable insights for developing transgenic crop breeding strategies for saline-alkaline soils.
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Affiliation(s)
- Yigong Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Yi Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Chun Wang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Jiangyuan Xiao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Mingqi Huang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Lu Zhuo
- College of Life Sciences, Shihezi University, Shihezi 832003, China.
| | - Daoyuan Zhang
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
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Ma H, Jiang P, Zhang X, Ma W, Cai Z, Sun Q. Effects of nitrogen fertilization combined with subsurface irrigation on alfalfa yield, water and nitrogen use efficiency, quality, and economic benefits. FRONTIERS IN PLANT SCIENCE 2024; 15:1339417. [PMID: 38348268 PMCID: PMC10859442 DOI: 10.3389/fpls.2024.1339417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024]
Abstract
Proper water and fertilizer management strategies are essential for alfalfa cultivation in arid areas. However, at present, the optimal amounts of subsurface irrigation and nitrogen (N) supply for alfalfa (Medicago sativa L.) cultivation are still unclear. Therefore, a field experiment was conducted in 2022 in Yinchuan, Ningxia, China, to explore the effects of different subsurface irrigation levels (W1, 50% of ETC (crop evapotranspiration); W2, 75% of ETC; W3, 100% of ETC) and N application rates (N0, 0 kg/ha; N1, 75 kg/ha; N2, 150 kg/ha; N3, 225 kg/ha; N4, 300 kg/ha) on alfalfa yield, crop water productivity (CWP), N use efficiency (NUE), quality, and economic benefits. Besides, the least squares method and multiple regression analysis were used to explore the optimal water and N combination for alfalfa cultivation under subsurface irrigation. The results showed that the alfalfa yield, crude ash content, and partial factor productivity from applied N (PFPN) were the highest under W2 level, but there was no difference in PFPN compared with that under W3 level. The branch number (BN), leaf area index (LAI), yield, CWP, irrigation water productivity (IWP), crude protein content (CPC), and economic benefits increased and then decreased with the increase of N application rate, reaching a maximum at the N2 or N3 level, while the NUE and PFPN decreased with the increase of N application rate. Considering the yield, CWP, NUE, quality, and economic benefits, W2N2 treatment was the optimal for alfalfa cultivation under subsurface irrigation. Besides, when the irrigation volume and N application rate were 69.8 ~ 88.7% of ETC and 145 ~ 190 kg/ha, respectively (confidence interval: 85%), the yield, CPC, and economic benefits reached more than 85% of the maximum. This study will provide technique reference for the water and N management in alfalfa cultivation in Northwest China.
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Affiliation(s)
- Hongxiu Ma
- College of Forestry and Prataculture, Ningxia University, Yinchuan, Ningxia, China
| | - Peng Jiang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, Ningxia, China
| | - Xiaojuan Zhang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, Ningxia, China
| | - Wenli Ma
- Ningxia Reclamation, Agricultural, Forestry, and Animal Husbandry Technology Promotion and Service Center, Yinchuan, Ningxia, China
| | - Zhanhong Cai
- Ningxia Reclamation, Agricultural, Forestry, and Animal Husbandry Technology Promotion and Service Center, Yinchuan, Ningxia, China
| | - Quan Sun
- College of Forestry and Prataculture, Ningxia University, Yinchuan, Ningxia, China
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Fan W, Xiao Y, Dong J, Xing J, Tang F, Shi F. Variety-driven rhizosphere microbiome bestows differential salt tolerance to alfalfa for coping with salinity stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1324333. [PMID: 38179479 PMCID: PMC10766110 DOI: 10.3389/fpls.2023.1324333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
Soil salinization is a global environmental issue and a significant abiotic stress that threatens crop production. Root-associated rhizosphere microbiota play a pivotal role in enhancing plant tolerance to abiotic stresses. However, limited information is available concerning the specific variations in rhizosphere microbiota driven by different plant genotypes (varieties) in response to varying levels of salinity stress. In this study, we compared the growth performance of three alfalfa varieties with varying salt tolerance levels in soils with different degrees of salinization. High-throughput 16S rRNA and ITS sequencing were employed to analyze the rhizosphere microbial communities. Undoubtedly, the increasing salinity significantly inhibited alfalfa growth and reduced rhizosphere microbial diversity. However, intriguingly, salt-tolerant varieties exhibited relatively lower susceptibility to salinity, maintaining more stable rhizosphere bacterial community structure, whereas the reverse was observed for salt-sensitive varieties. Bacillus emerged as the dominant species in alfalfa's adaptation to salinity stress, constituting 21.20% of the shared bacterial genera among the three varieties. The higher abundance of Bacillus, Ensifer, and Pseudomonas in the rhizosphere of salt-tolerant alfalfa varieties is crucial in determining their elevated salt tolerance. As salinity levels increased, salt-sensitive varieties gradually accumulated a substantial population of pathogenic fungi, such as Fusarium and Rhizoctonia. Furthermore, rhizosphere bacteria of salt-tolerant varieties exhibited increased activity in various metabolic pathways, including biosynthesis of secondary metabolites, carbon metabolism, and biosynthesis of amino acids. It is suggested that salt-tolerant alfalfa varieties can provide more carbon sources to the rhizosphere, enriching more effective plant growth-promoting bacteria (PGPB) such as Pseudomonas to mitigate salinity stress. In conclusion, our results highlight the variety-mediated enrichment of rhizosphere microbiota in response to salinity stress, confirming that the high-abundance enrichment of specific dominant rhizosphere microbes and their vital roles play a significant role in conferring high salt adaptability to these varieties.
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Affiliation(s)
- Wenqiang Fan
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanzi Xiao
- College of Agriculture and Forestry, Hulunbuir University, Hulunber, China
| | - Jiaqi Dong
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Xing
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Fang Tang
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Fengling Shi
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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Shao A, Fan S, Xu X, Wang W, Fu J. Identification and evolution analysis of YUCCA genes of Medicago sativa and Medicago truncatula and their expression profiles under abiotic stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1268027. [PMID: 37701802 PMCID: PMC10494245 DOI: 10.3389/fpls.2023.1268027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023]
Abstract
The YUCCAs (YUC) are functionally identified flavin-containing monooxidases (FMOs) in plants that act as an important rate-limiting enzyme functioning in the auxin synthesis IPA (indole-3-pyruvic acid) pathway. In this study, 12 MsYUCs and 15 MtYUCs containing characteristic conserved motifs were identified in M. sativa (Medicago sativa L.) and M. truncatula (Medicago truncatula Gaertn.), respectively. Phylogenetic analysis revealed that YUC proteins underwent an evolutionary divergence. Both tandem and segmental duplication events were presented in MsYUC and MtYUC genes. Comparative syntenic maps of M. sativa with M. truncatula, Arabidopsis (Arabidopsis thaliana), or rice (Oryza sativa L.) were constructed to illustrate the evolution relationship of the YUC gene family. A large number of cis-acting elements related to stress response and hormone regulation were revealed in the promoter sequences of MsYUCs. Expression analysis showed that MsYUCs had a tissue-specific, genotype-differential expression and a differential abiotic stress response pattern based on transcriptome data analysis of M. sativa online. In addition, RT-qPCR confirmed that salt stress significantly induced the expression of MsYUC1/MsYUC10 but significantly inhibited MsYUC2/MsYUC3 expression and the expression of MsYUC10/MsYUC11/MsYUC12 was significantly induced by cold treatment. These results could provide valuable information for functional analysis of YUC genes via gene engineering of the auxin synthetic IPA pathway in Medicago.
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Affiliation(s)
| | | | | | - Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - Jinmin Fu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
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Lin S, Medina CA, Wang G, Combs D, Shewmaker G, Fransen S, Llewellyn D, Norberg S, Yu LX. Identification of genetic loci associated with five agronomic traits in alfalfa using multi-environment trials. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:121. [PMID: 37119337 DOI: 10.1007/s00122-023-04364-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
The use of multi-environment trials to test yield-related traits in a diverse alfalfa panel allowed to find multiple molecular markers associated with complex agronomic traits. Yield is one of the most important target traits in alfalfa breeding; however, yield is a complex trait affected by genetic and environmental factors. In this study, we used multi-environment trials to test yield-related traits in a diverse panel composed of 200 alfalfa accessions and varieties. Phenotypic data of maturity stage measured as mean stage by count (MSC), dry matter content, plant height (PH), biomass yield (Yi), and fall dormancy (FD) were collected in three locations in Idaho, Oregon, and Washington from 2018 to 2020. Single-trial and stagewise analyses were used to obtain estimated trait means of entries by environment. The plants were genotyped using a genotyping by sequencing approach and obtained a genotypic matrix with 97,345 single nucleotide polymorphisms. Genome-wide association studies identified a total of 84 markers associated with the traits analyzed. Of those, 29 markers were in noncoding regions and 55 markers were in coding regions. Ten significant SNPs at the same locus were associated with FD and they were linked to a gene annotated as a nuclear fusion defective 4-like (NFD4). Additional SNPs associated with MSC, PH, and Yi were annotated as transcription factors such as Cysteine3Histidine (C3H), Hap3/NF-YB family, and serine/threonine-protein phosphatase 7 proteins, respectively. Our results provide insight into the genetic factors that influence alfalfa maturity, yield, and dormancy, which is helpful to speed up the genetic gain toward alfalfa yield improvement.
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Affiliation(s)
- Sen Lin
- USA Department of Agriculture - Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, USA
| | - Cesar A Medina
- USA Department of Agriculture - Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, USA
| | - Guojie Wang
- Department of Crop and Soil Science, Oregon State University, LaGrande, OR, USA
| | - David Combs
- Department of Dairy Science, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Steve Fransen
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Don Llewellyn
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Steven Norberg
- Franklin County Extension Office, Washington State University, Pasco, WA, USA.
| | - Long-Xi Yu
- USA Department of Agriculture - Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, USA.
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Zhou F, Matthew C, Yang P, Huang Y, Nie B, Nan Z. Leaf morphology, functional trait and altitude response in perennial vetch (Vicia unijuga A. Braun), alfalfa (Medicago sativa L.) and sainfoin (Onobrychis viciifolia Scop.). PLANTA 2023; 257:75. [PMID: 36879140 DOI: 10.1007/s00425-023-04098-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Species have plasticity across altitude gradients in leaf morphology and function, and their response to high altitude conditions was mainly reflected in leaf cell metabolism and gas exchange. Leaf morphological and functional adaptation to altitude has received research attention in recent years, but there are no studies for forage legumes. Here we report differences in 39 leaf morphology and functional traits of three leguminous forages (alfalfa, sainfoin and perennial vetch) at three sites in Gansu Province, China, ranging from 1768 to 3074 m altitude to provide information for potential use in breeding programmes. With increasing altitude, plant water status increased, reflecting increase in soil water content and decreased average temperature, which lead to leaf intercellular CO2 concentration. Stomatal conductance and evapotranspiration increased significantly but water-use efficiency decreased. At high altitude, ΦPSII decreased but non-photochemical quenching and chlorophyll a:b ratio increased while spongy mesophyll tissue and leaf thickness increased. These changes may be due to UV or low-temperature damage of leaf protein and metabolic cost of plant protection or defence responses. Contrary to many other studies, leaf mass per area decreased significantly at higher altitude. This was consistent with predictions under the worldwide leaf economic spectrum on the basis that soil nutrients increased with increasing altitude. The key species differences were more irregularly shaped epidermal cells and larger stomatal size in perennial vetch compared to alfalfa or sainfoin that enhanced gas exchange and photosynthesis by generating mechanical force, increasing guard cell turgor, and promoting stomatal operation. The lower adaxial stomatal density also enhanced water-use efficiency. These adaptations might confer perennial vetch an advantage in environments with extreme diurnal temperature fluctuation or in frigid conditions.
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Affiliation(s)
- Fangfang Zhou
- State Key Laboratory of Grassland Agroecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, Gansu, China
| | - Cory Matthew
- School of Agriculture and Environment, College of Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Pengfei Yang
- School of Life Sciences, Lanzhou University, Lanzhou, 730020, Gansu, China
| | - Yafeng Huang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230031, Anhui, China
| | - Bin Nie
- State Key Laboratory of Grassland Agroecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, Gansu, China
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agroecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, Gansu, China.
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Filho CCF, Andrade MHML, Nunes JAR, Jarquin DH, Rios EF. Genomic prediction for complex traits across multiples harvests in alfalfa (Medicago sativa L.) is enhanced by enviromics. THE PLANT GENOME 2023:e20306. [PMID: 36815221 DOI: 10.1002/tpg2.20306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/17/2022] [Indexed: 06/18/2023]
Abstract
Breeding for dry matter yield and persistence in alfalfa (Medicago sativa L.) can take several years as these traits must be evaluated under multiple harvests. Therefore, genotype-by-harvest interaction should be incorporated into genomic prediction models to explore genotypes' adaptability and stability. In this study, we investigated how enviromics could help to predict the genotypic performance under multiharvest alfalfa breeding trials by evaluating 177 families across 11 harvests under four cross-validation scenarios. All scenarios were analyzed using six models in a Bayesian mixed model framework. Our results demonstrate that models accounting to the enviromics information led to an increase of genetic variance and a decrease in the error variance, indicating better biological explanation when the enviromic information was incorporated. Furthermore, models that accounted for enviromic data led to higher predictive ability (PA) in a reduced number of harvests used in the training data set. The best enviromic models (M2 and M3) outperformed the base model (GBLUP model-M0) for predicting adaptability and persistence across all cross-validation scenarios. Incorporating environmental covariates also provided higher PA for persistence compared with the base model, as predictions increased from 0 to 0.16, 0.20, 0.56, and 0.46 for CV00, CV1, CV0, and CV2. The results also demonstrate that GBLUP without enviromics term has low power to predict persistence, thus the adoption of enviromics is a cheap and efficient alternative to increase accuracy and biological meaning.
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Affiliation(s)
| | | | - José Airton Rodrigues Nunes
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
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Domokos-Szabolcsy É, Yavuz SR, Picoli E, Fári MG, Kovács Z, Tóth C, Kaszás L, Alshaal T, Elhawat N. Green Biomass-Based Protein for Sustainable Feed and Food Supply: An Overview of Current and Future Prospective. Life (Basel) 2023; 13:307. [PMID: 36836666 PMCID: PMC9966994 DOI: 10.3390/life13020307] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
It is necessary to develop and deploy novel protein production to allow the establishment of a sustainable supply for both humans and animals, given the ongoing expansion of protein demand to meet the future needs of the increased world population and high living standards. In addition to plant seeds, green biomass from dedicated crops or green agricultural waste is also available as an alternative source to fulfill the protein and nutrient needs of humans and animals. The development of extraction and precipitation methods (such as microwave coagulation) for chloroplast and cytoplasmic proteins, which constitute the bulk of leaf protein, will allow the production of leaf protein concentrates (LPC) and protein isolates (LPI). Obtained LPC serves as a sustainable alternative source of animal-based protein besides being an important source of many vital phytochemicals, including vitamins and substances with nutritional and pharmacological effects. Along with it, the production of LPC, directly or indirectly, supports sustainability and circular economy concepts. However, the quantity and quality of LPC largely depend on several factors, including plant species, extraction and precipitation techniques, harvest time, and growing season. This paper provides an overview of the history of green biomass-derived protein from the early green fodder mill concept by Károly Ereky to the state-of-art of green-based protein utilization. It highlights potential approaches for enhancing LPC production, including dedicated plant species, associated extraction methods, selection of optimal technologies, and best combination approaches for improving leaf protein isolation.
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Affiliation(s)
- Éva Domokos-Szabolcsy
- Department of Applied Plant Biology, University of Debrecen, Böszörményi Str. 138, 4032 Debrecen, Hungary
| | - Seckin Reyhan Yavuz
- Department of Applied Plant Biology, University of Debrecen, Böszörményi Str. 138, 4032 Debrecen, Hungary
| | - Edgard Picoli
- Department of Plant Biology, Federal University of Viçosa, Viçosa 36570-900, Brazil
| | - Miklós Gabor Fári
- Department of Applied Plant Biology, University of Debrecen, Böszörményi Str. 138, 4032 Debrecen, Hungary
| | - Zoltán Kovács
- Department of Applied Plant Biology, University of Debrecen, Böszörményi Str. 138, 4032 Debrecen, Hungary
| | - Csaba Tóth
- Department of Applied Plant Biology, University of Debrecen, Böszörményi Str. 138, 4032 Debrecen, Hungary
| | - László Kaszás
- Department of Applied Plant Biology, University of Debrecen, Böszörményi Str. 138, 4032 Debrecen, Hungary
| | - Tarek Alshaal
- Department of Applied Plant Biology, University of Debrecen, Böszörményi Str. 138, 4032 Debrecen, Hungary
- Department of Biological and Environmental Sciences, Faculty of Home Economic, Al-Azhar University, Tanta 31732, Egypt
| | - Nevien Elhawat
- Department of Applied Plant Biology, University of Debrecen, Böszörményi Str. 138, 4032 Debrecen, Hungary
- Soil and Water Science Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
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Subedi U, Burton Hughes K, Chen G, Hannoufa A, Singer SD. Eliciting Targeted Mutations in Medicago sativa Using CRISPR/Cas9-Mediated Genome Editing: A Potential Tool for the Improvement of Disease Resistance. Methods Mol Biol 2023; 2659:219-239. [PMID: 37249896 DOI: 10.1007/978-1-0716-3159-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) has become a breeding tool of choice for eliciting targeted genetic alterations in crop species as a means of improving a wide range of agronomic traits, including disease resistance, in recent years. With the recent development of CRISPR/Cas9 technology in Medicago sativa (alfalfa), which is an important perennial forage legume grown worldwide, its use for the enhancement of pathogen resistance is almost certainly on the horizon. In this chapter, we present detailed procedures for the generation of a single nonhomologous end-joining-derived indel at a precise genomic locus of alfalfa via CRISPR/Cas9. This method encompasses crucial steps in this process, including guide RNA design, binary CRISPR vector construction, Agrobacterium-mediated transformation of alfalfa explants, and molecular assessments of transformed genotypes for transgene and edit identification.
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Affiliation(s)
- Udaya Subedi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Kimberley Burton Hughes
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Abdelali Hannoufa
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Stacy D Singer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
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Kumar P, Singh J, Kaur G, Adunola PM, Biswas A, Bazzer S, Kaur H, Kaur I, Kaur H, Sandhu KS, Vemula S, Kaur B, Singh V, Tseng TM. OMICS in Fodder Crops: Applications, Challenges, and Prospects. Curr Issues Mol Biol 2022; 44:5440-5473. [PMID: 36354681 PMCID: PMC9688858 DOI: 10.3390/cimb44110369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 09/08/2024] Open
Abstract
Biomass yield and quality are the primary targets in forage crop improvement programs worldwide. Low-quality fodder reduces the quality of dairy products and affects cattle's health. In multipurpose crops, such as maize, sorghum, cowpea, alfalfa, and oat, a plethora of morphological and biochemical/nutritional quality studies have been conducted. However, the overall growth in fodder quality improvement is not on par with cereals or major food crops. The use of advanced technologies, such as multi-omics, has increased crop improvement programs manyfold. Traits such as stay-green, the number of tillers per plant, total biomass, and tolerance to biotic and/or abiotic stresses can be targeted in fodder crop improvement programs. Omic technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, provide an efficient way to develop better cultivars. There is an abundance of scope for fodder quality improvement by improving the forage nutrition quality, edible quality, and digestibility. The present review includes a brief description of the established omics technologies for five major fodder crops, i.e., sorghum, cowpea, maize, oats, and alfalfa. Additionally, current improvements and future perspectives have been highlighted.
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Affiliation(s)
- Pawan Kumar
- Agrotechnology Division, Council of Scientific and Industrial Research-Institute of Himalayan Bioresource Technology, Palampur 176061, India
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India
| | - Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India
- Krishi Vigyan Kendra, Guru Angad Dev Veterinary and Animal Science University, Barnala 148107, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | | | - Anju Biswas
- Agronomy Department, University of Florida, Gainesville, FL 32611, USA
| | - Sumandeep Bazzer
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, WA 57007, USA
| | - Harpreet Kaur
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88001, USA
| | - Ishveen Kaur
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Harpreet Kaur
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Shailaja Vemula
- Agronomy Department, UF/IFAS Research and Education Center, Belle Glade, FL 33430, USA
| | - Balwinder Kaur
- Department of Entomology, UF/IFAS Research and Education Center, Belle Glade, FL 33430, USA
| | - Varsha Singh
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS 39759, USA
| | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS 39759, USA
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13
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Jiang X, Yang X, Zhang F, Yang T, Yang C, He F, Gao T, Wang C, Yang Q, Wang Z, Kang J. Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development. BMC PLANT BIOLOGY 2022; 22:485. [PMID: 36217123 PMCID: PMC9552516 DOI: 10.1186/s12870-022-03864-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Leaf size affects crop canopy morphology and photosynthetic efficiency, which can influence forage yield and quality. It is of great significance to mine the key genes controlling leaf development for breeding new alfalfa varieties. In this study, we mapped leaf length (LL), leaf width (LW), and leaf area (LA) in an F1 mapping population derived from a cultivar named ZhongmuNo.1 with larger leaf area and a landrace named Cangzhou with smaller leaf area. RESULTS This study showed that the larger LW was more conducive to increasing LA. A total of 24 significant quantitative trait loci (QTL) associated with leaf size were identified on both the paternal and maternal linkage maps. Among them, nine QTL explained about 11.50-22.45% phenotypic variation. RNA-seq analysis identified 2,443 leaf-specific genes and 3,770 differentially expressed genes. Combining QTL mapping, RNA-seq alalysis, and qRT-PCR, we identified seven candidate genes associated with leaf development in five major QTL regions. CONCLUSION Our study will provide a theoretical basis for marker-assisted breeding and lay a foundation for further revealing molecular mechanism of leaf development in alfalfa.
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Affiliation(s)
- Xueqian Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xijiang Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianhui Yang
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Ningxia, China
| | - Changfu Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ting Gao
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Ningxia, China
| | - Chuan Wang
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Ningxia, China
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Zhang F, Kang J, Long R, Li M, Sun Y, He F, Jiang X, Yang C, Yang X, Kong J, Wang Y, Wang Z, Zhang Z, Yang Q. Application of machine learning to explore the genomic prediction accuracy of fall dormancy in autotetraploid alfalfa. HORTICULTURE RESEARCH 2022; 10:uhac225. [PMID: 36643744 PMCID: PMC9832841 DOI: 10.1093/hr/uhac225] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/25/2022] [Indexed: 06/17/2023]
Abstract
Fall dormancy (FD) is an essential trait to overcome winter damage and for alfalfa (Medicago sativa) cultivar selection. The plant regrowth height after autumn clipping is an indirect way to evaluate FD. Transcriptomics, proteomics, and quantitative trait locus mapping have revealed crucial genes correlated with FD; however, these genes cannot predict alfalfa FD very well. Here, we conducted genomic prediction of FD using whole-genome SNP markers based on machine learning-related methods, including support vector machine (SVM) regression, and regularization-related methods, such as Lasso and ridge regression. The results showed that using SVM regression with linear kernel and the top 3000 genome-wide association study (GWAS)-associated markers achieved the highest prediction accuracy for FD of 64.1%. For plant regrowth height, the prediction accuracy was 59.0% using the 3000 GWAS-associated markers and the SVM linear model. This was better than the results using whole-genome markers (25.0%). Therefore, the method we explored for alfalfa FD prediction outperformed the other models, such as Lasso and ElasticNet. The study suggests the feasibility of using machine learning to predict FD with GWAS-associated markers, and the GWAS-associated markers combined with machine learning would benefit FD-related traits as well. Application of the methodology may provide potential targets for FD selection, which would accelerate genetic research and molecular breeding of alfalfa with optimized FD.
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Affiliation(s)
- Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China, 100193
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA, 99163
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China, 100193
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China, 100193
| | - Mingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China, 100193
| | - Yan Sun
- Department of Turf Science and Engineering, College of Grassland Science and Technology, China Agricultural University, Beijing, China, 100193
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China, 100193
| | - Xueqian Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China, 100193
| | - Changfu Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China, 100193
| | - Xijiang Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China, 100193
| | - Jie Kong
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China, 100193
| | - Yiwen Wang
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia, 3052
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China, 100193
| | - Zhiwu Zhang
- Corresponding author: Zhiwu Zhang (, Phone (Office): 509-335-2899, Fax: 509-335-8674) or Qingchuan Yang (, Phone: 010-62815996, Fax: 010-62815996)
| | - Qingchuan Yang
- Corresponding author: Zhiwu Zhang (, Phone (Office): 509-335-2899, Fax: 509-335-8674) or Qingchuan Yang (, Phone: 010-62815996, Fax: 010-62815996)
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15
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Zhou X, Li X, Zhang X, Yin D, Wang J, Zhao Y. Construction of a high-density genetic map and localization of grazing-tolerant QTLs in Medicago falcata L. FRONTIERS IN PLANT SCIENCE 2022; 13:985603. [PMID: 36262664 PMCID: PMC9574245 DOI: 10.3389/fpls.2022.985603] [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: 07/04/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Using genomic DNA from 79 F1 plants resulted from a crossing between parents with strong and weak grazing tolerance in Medicago falcata L., we generated an EcoRI restriction site-associated DNA (RAD) sequencing library. After sequencing and assembly, a high-density genetic map with high-quality SNP markers was constructed, with a total length of 1312.238 cM and an average density of 0.844 SNP/cM. METHODS The phenotypic traits of 79 F1 families were observed and the QTLS of 6 traits were analyzed by interval mapping. RESULTS Sixty three QTLs were identified for seven traits with LOD values from 3 to 6 and the contribution rates from 15% to 30%. Among the 63 QTLs, 17 were for natural shoot height, 12 for rhizome Length, 10 for Shoot canopy diameter, 9 for Basal plant diameter, 6 for stem number, 5 for absolute shoot height, and 4 for rhizome width. These QTLs were concentrated on LG2, LG4, LG5, LG7, and LG8. LG6 had only 6 QTLs. According to the results of QTL mapping, comparison of reference genomes, and functional annotation, 10 candidate genes that may be related to grazing tolerance were screened. qRT-PCR analysis showed that two candidate genes (LOC11412291 and LOC11440209) may be the key genes related to grazing tolerance of M. falcata. CONCLUSION The identified trait-associated QTLs and candidate genes in this study will provide a solid foundation for future molecular breeding for enhanced grazing-tolerance in M. falcata.
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Murad Leite Andrade MH, Acharya JP, Benevenuto J, de Bem Oliveira I, Lopez Y, Munoz P, Resende MFR, Rios EF. Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks. THE PLANT GENOME 2022; 15:e20235. [PMID: 35818699 DOI: 10.1002/tpg2.20235] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Genomic selection (GS) has proven to be an effective method to increase genetic gain rates and accelerate breeding cycles in many crop species. However, its implementation requires large investments to phenotype of the training population and for routine genotyping. Alfalfa (Medicago sativa L.) is one of the major cultivated forage legumes, showing high-quality nutritional value. Alfalfa breeding is usually carried out by phenotypic recurrent selection and is commonly done at the family level. The application of GS in alfalfa could be simplified and less costly by genotyping and phenotyping families in bulks. For this study, an alfalfa reference population composed of 142 full-sib and 35 half-sib families was bulk-genotyped using target enrichment sequencing and phenotyped for dry matter yield (DMY) and canopy height (CH) in Florida, USA. Genotyping of the family bulks with 17,707 targeted probes resulted in 114,945 single-nucleotide polymorphisms. The markers revealed a population structure that matched the mating design, and the linkage disequilibrium slowly decayed in this breeding population. After exploring multiple prediction scenarios, a strategy was proposed including data from multiple harvests and accounting for the G×E in the training population, which led to a higher predictive ability of up to 38 and 24% for DMY and CH, respectively. Although this study focused on the implementation of GS in alfalfa families, the bulk methodology and the prediction schemes used herein could guide future studies in alfalfa and other crops bred in bulks.
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Affiliation(s)
| | - Janam P Acharya
- Agronomy Dep., Univ. of Florida, Gainesville, FL, 32611, USA
| | - Juliana Benevenuto
- Horticultural Sciences Dep., Univ. of Florida, Gainesville, FL, 32611, USA
| | | | - Yolanda Lopez
- Agronomy Dep., Univ. of Florida, Gainesville, FL, 32611, USA
| | - Patricio Munoz
- Horticultural Sciences Dep., Univ. of Florida, Gainesville, FL, 32611, USA
| | - Marcio F R Resende
- Horticultural Sciences Dep., Univ. of Florida, Gainesville, FL, 32611, USA
| | - Esteban F Rios
- Agronomy Dep., Univ. of Florida, Gainesville, FL, 32611, USA
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17
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Du W, Yang J, Li Q, Su Q, Yi D, Pang Y. Genome-Wide Identification and Characterization of Growth Regulatory Factor Family Genes in Medicago. Int J Mol Sci 2022; 23:ijms23136905. [PMID: 35805911 PMCID: PMC9266564 DOI: 10.3390/ijms23136905] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/05/2022] [Accepted: 06/07/2022] [Indexed: 12/10/2022] Open
Abstract
Growth Regulatory Factors (GRF) are plant-specific transcription factors that play critical roles in plant growth and development as well as plant tolerance against stress. In this study, a total of 16 GRF genes were identified from the genomes of Medicago truncatula and Medicago sativa. Multiple sequence alignment analysis showed that all these members contain conserved QLQ and WRC domains. Phylogenetic analysis suggested that these GRF proteins could be classified into five clusters. The GRF genes showed similar exon–intron organizations and similar architectures in their conserved motifs. Many stress-related cis-acting elements were found in their promoter region, and most of them were related to drought and defense response. In addition, analyses on microarray and transcriptome data indicated that these GRF genes exhibited distinct expression patterns in various tissues or in response to drought and salt treatments. In particular, qPCR results showed that the expression levels of gene pairs MtGRF2–MsGRF2 and MtGRF6–MsGRF6 were significantly increased under NaCl and mannitol treatments, indicating that they are most likely involved in salt and drought stress tolerance. Collectively, our study is valuable for further investigation on the function of GRF genes in Medicago and for the exploration of GRF genes in the molecular breeding of highly resistant M. sativa.
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Affiliation(s)
- Wenxuan Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Junfeng Yang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China;
| | - Qian Li
- West Arid Region Grassland Resource and Ecology Key Laboratory, College of Grassland and Environmental Sciences, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Qian Su
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010010, China;
| | - Dengxia Yi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (D.Y.); (Y.P.)
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (D.Y.); (Y.P.)
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18
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Yuan Y, Yu J, Kong L, Zhang W, Hou X, Cui G. Genome-wide investigation of the PLD gene family in alfalfa (Medicago sativa L.): identification, analysis and expression. BMC Genomics 2022; 23:243. [PMID: 35350974 PMCID: PMC8962232 DOI: 10.1186/s12864-022-08424-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Background External environmental factors, such as salt, alkali and drought, severely limit the acreage and yield of alfalfa. The mining of tolerance-related genes in alfalfa and improving the stress resistance of this plant are essential for increasing alfalfa yield. PLD is the main phospholipid hydrolase in plants and plays an important role in plant growth, development, signaling, and resistance to adverse stress. With the availability of whole genome sequences, the annotation and expression of PLDs in alfalfa can now be achieved. At present, few studies have investigated PLDs in alfalfa. Here, we conducted a study of PLDs in alfalfa and identified and analyzed the expression pattern of PLDs under different treatments. Results Fifty-nine MsPLDs were identified in alfalfa and classified into six subtypes: MsPLDα, β, γ, δ and ε belong to the C2-PLD subfamily, and MsPLDζ belongs to the PXPH-PLD subfamily. Members of the same PLD subtype have similar physicochemical properties, sequence structure and domains, but their cis-acting elements are different. A qRT-PCR analysis revealed that MsPLDs are expressed in multiple tissues. MsPLDs can respond to alkali, drought, ABA, IAA, and GA3 treatments and particularly to salt stress. Different expression patterns were found for the same gene under different treatments and different genes under the same treatment. Expression of MsPLD05 improved salt tolerance in yeast. Conclusion This study represents the first genome-wide characterization of MsPLDs in alfalfa. Most MsPLDs are expressed mainly in mature leaves and respond positively to abiotic stresses and hormonal treatments. This study further expands the resistance gene pool in legume forage grasses and provides a reference for further in-depth study of MsPLDs in alfalfa. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08424-9.
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Singh L, Pierce C, Santantonio N, Steiner R, Miller D, Reich J, Ray I. Validation of DNA marker-assisted selection for forage biomass productivity under deficit irrigation in alfalfa. THE PLANT GENOME 2022; 15:e20195. [PMID: 35178866 DOI: 10.1002/tpg2.20195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Drought and limited irrigation resources threaten agricultural sustainability in many regions of the world. Application of genomic-based breeding strategies may benefit crop variety development for these environments. Here, we provide a first report on the effect of deploying DNA marker-assisted selection (MAS) for the drought resilience quantitative trait in alfalfa (Medicago sativa L.). The goals of this study were to validate the effect of several quantitative trait loci (QTL) associated with alfalfa forage and crown-root (CR) biomass during drought and to determine their potential to improve forage yield of elite germplasm under water-limited conditions. Marker assisted selection was employed to introgress favorable or unfavorable DNA marker alleles affiliated with 10 biomass QTL into three elite backgrounds. Thirty-two populations were developed and evaluated for forage productivity over 3 yr under continuous deficit irrigation management in New Mexico, USA. Significant yield differences (ranging from -13 to 26%) were detected among some MAS-derived populations in all three elite backgrounds. Application of QTL MAS generally resulted in expected phenotypic responses within an elite genetic background that was similar to that in which the QTL were originally identified. However, relative performance of the populations varied substantially across the three genetic backgrounds. These outcomes indicate that QTL MAS can significantly affect forage productivity of elite alfalfa germplasm in drought-stressed environments. However, if biomass QTL are detected in donor germplasm that is genetically dissimilar to targeted elite populations, characterization of donor alleles may be warranted within elite backgrounds of interest to confirm their phenotypic effects prior to implementing MAS-based breeding.
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Affiliation(s)
- Lovepreet Singh
- Dep. of Plant and Environmental Sciences, New Mexico State Univ., Las Cruces, NM, 88003, USA
- Dep. of Plant Science and Landscape Architecture, Univ. of Maryland, College Park, MD, 20742, USA
| | - Chris Pierce
- Dep. of Plant and Environmental Sciences, New Mexico State Univ., Las Cruces, NM, 88003, USA
| | - Nicholas Santantonio
- Dep. of Plant and Environmental Sciences, New Mexico State Univ., Las Cruces, NM, 88003, USA
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Robert Steiner
- Dep. of Economics, Applied Statistics and International Business, New Mexico State Univ., Las Cruces, NM, 88003, USA
| | - Don Miller
- Cal/West Seeds, Woodland, CA, 95695, USA
- Alforex Seeds, Woodland, CA, 95695, USA
| | - Jon Reich
- Cal/West Seeds, Woodland, CA, 95695, USA
- Canaan Agricultural Consulting LLC, Woodland, CA, 95695, USA
| | - Ian Ray
- Dep. of Plant and Environmental Sciences, New Mexico State Univ., Las Cruces, NM, 88003, USA
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20
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Chiurazzi MJ, Nørrevang AF, García P, Cerdán PD, Palmgren M, Wenkel S. Controlling flowering of Medicago sativa (alfalfa) by inducing dominant mutations. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:205-214. [PMID: 34761872 PMCID: PMC9303315 DOI: 10.1111/jipb.13186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Breeding plants with polyploid genomes is challenging because functional redundancy hampers the identification of loss-of-function mutants. Medicago sativa is tetraploid and obligate outcrossing, which together with inbreeding depression complicates traditional breeding approaches in obtaining plants with a stable growth habit. Inducing dominant mutations would provide an alternative strategy to introduce domestication traits in plants with high gene redundancy. Here we describe two complementary strategies to induce dominant mutations in the M. sativa genome and how they can be relevant in the control of flowering time. First, we outline a genome-engineering strategy that harnesses the use of microProteins as developmental regulators. MicroProteins are small proteins that appeared during genome evolution from genes encoding larger proteins. Genome-engineering allows us to retrace evolution and create microProtein-coding genes de novo. Second, we provide an inventory of genes regulated by microRNAs that control plant development. Making respective gene transcripts microRNA-resistant by inducing point mutations can uncouple microRNA regulation. Finally, we investigated the recently published genomes of M. sativa and provide an inventory of breeding targets, some of which, when mutated, are likely to result in dominant traits.
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Affiliation(s)
- Maurizio Junior Chiurazzi
- NovoCrops CenterUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
- Copenhagen Plant Science CentreUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
- Department of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
| | - Anton Frisgaard Nørrevang
- NovoCrops CenterUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
- Copenhagen Plant Science CentreUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
- Department of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
| | - Pedro García
- Fundación Instituto LeloirIIBBA‐CONICETAvenida Patricias Argentinas 435Buenos Aires1405Argentina
| | - Pablo D. Cerdán
- Fundación Instituto LeloirIIBBA‐CONICETAvenida Patricias Argentinas 435Buenos Aires1405Argentina
| | - Michael Palmgren
- NovoCrops CenterUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
- Copenhagen Plant Science CentreUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
- Department of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
| | - Stephan Wenkel
- NovoCrops CenterUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
- Copenhagen Plant Science CentreUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
- Department of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsensvej 40Frederiksberg C1871Denmark
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21
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Long R, Zhang F, Zhang Z, Li M, Chen L, Wang X, Liu W, Zhang T, Yu LX, He F, Jiang X, Yang X, Yang C, Wang Z, Kang J, Yang Q. Genome assembly of alfalfa cultivar zhongmu-4 and identification of SNPs associated with agronomic traits. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:14-28. [PMID: 35033678 PMCID: PMC9510860 DOI: 10.1016/j.gpb.2022.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 12/21/2022]
Abstract
Alfalfa (Medicago sativa L.) is the most important legume forage crop worldwide with high nutritional value and yield. For a long time, the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic traits. We herein reported the de novo assembly of the allele-aware chromosome-level genome of Zhongmu-4, a cultivar widely cultivated in China, and a comprehensive database of genomic variations based on resequencing of 220 germplasms. Approximate 2.74 Gb contigs (N50 of 2.06 Mb), accounting for 88.39% of the estimated genome, were assembled, and 2.56 Gb contigs were anchored to 32 pseudo-chromosomes. A total of 34,922 allelic genes were identified from the allele-aware genome. We observed the expansion of gene families, especially those related to the nitrogen metabolism, and the increase of repetitive elements including transposable elements, which probably resulted in the increase of Zhongmu-4 genome compared with Medicago truncatula. Population structure analysis revealed that the accessions from Asia and South America had relatively lower genetic diversity than those from Europe, suggesting that geography may influence alfalfa genetic divergence during local adaption. Genome-wide association studies identified 101 single nucleotide polymorphisms (SNPs) associated with 27 agronomic traits. Two candidate genes were predicted to be correlated with fall dormancy and salt response. We believe that the allele-aware chromosome-level genome sequence of Zhongmu-4 combined with the resequencing data of the diverse alfalfa germplasms will facilitate genetic research and genomics-assisted breeding in variety improvement of alfalfa.
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Affiliation(s)
- Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fan Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99163, United States
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99163, United States
| | - Mingna Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lin Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wenwen Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tiejun Zhang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant and Germplasm Introduction and Testing Research, Prosser, WA, 99350, United States
| | - Fei He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xueqian Jiang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xijiang Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Changfu Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhen Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Junmei Kang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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22
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Chen L, He F, Long R, Zhang F, Li M, Wang Z, Kang J, Yang Q. A global alfalfa diversity panel reveals genomic selection signatures in Chinese varieties and genomic associations with root development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1937-1951. [PMID: 34487430 DOI: 10.1111/jipb.13172] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/03/2021] [Indexed: 05/04/2023]
Abstract
Alfalfa (Medicago sativa L.) is an important forage crop worldwide. However, little is known about the effects of breeding status and different geographical populations on alfalfa improvement. Here, we sequenced 220 alfalfa core germplasms and determined that Chinese alfalfa cultivars form an independent group, as evidenced by comparisons of FST values between different subgroups, suggesting that geographical origin plays an important role in group differentiation. By tracing the influence of geographical regions on the genetic diversity of alfalfa varieties in China, we identified 350 common candidate genetic regions and 548 genes under selection. We also defined 165 loci associated with 24 important traits from genome-wide association studies. Of those, 17 genomic regions closely associated with a given phenotype were under selection, with the underlying haplotypes showing significant differences between subgroups of distinct geographical origins. Based on results from expression analysis and association mapping, we propose that 6-phosphogluconolactonase (MsPGL) and a gene encoding a protein with NHL domains (MsNHL) are critical candidate genes for root growth. In conclusion, our results provide valuable information for alfalfa improvement via molecular breeding.
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Affiliation(s)
- Lin Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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23
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Singer SD, Subedi U, Lehmann M, Burton Hughes K, Feyissa BA, Hannoufa A, Shan B, Chen G, Kader K, Ortega Polo R, Schwinghamer T, Kaur Dhariwal G, Acharya S. Identification of Differential Drought Response Mechanisms in Medicago sativa subsp. sativa and falcata through Comparative Assessments at the Physiological, Biochemical, and Transcriptional Levels. PLANTS 2021; 10:plants10102107. [PMID: 34685916 PMCID: PMC8539336 DOI: 10.3390/plants10102107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/23/2021] [Accepted: 10/01/2021] [Indexed: 12/12/2022]
Abstract
Alfalfa (Medicago sativa L.) is an extensively grown perennial forage legume, and although it is relatively drought tolerant, it consumes high amounts of water and depends upon irrigation in many regions. Given the progressive decline in water available for irrigation, as well as an escalation in climate change-related droughts, there is a critical need to develop alfalfa cultivars with improved drought resilience. M. sativa subsp. falcata is a close relative of the predominantly cultivated M. sativa subsp. sativa, and certain accessions have been demonstrated to exhibit superior performance under drought. As such, we endeavoured to carry out comparative physiological, biochemical, and transcriptomic evaluations of an as of yet unstudied drought-tolerant M. sativa subsp. falcata accession (PI 641381) and a relatively drought-susceptible M. sativa subsp. sativa cultivar (Beaver) to increase our understanding of the molecular mechanisms behind the enhanced ability of falcata to withstand water deficiency. Our findings indicate that unlike the small number of falcata genotypes assessed previously, falcata PI 641381 may exploit smaller, thicker leaves, as well as an increase in the baseline transcriptional levels of genes encoding particular transcription factors, protective proteins, and enzymes involved in the biosynthesis of stress-related compounds. These findings imply that different falcata accessions/genotypes may employ distinct drought response mechanisms, and the study provides a suite of candidate genes to facilitate the breeding of alfalfa with enhanced drought resilience in the future.
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Affiliation(s)
- Stacy D. Singer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (U.S.); (M.L.); (K.B.H.); (K.K.); (R.O.P.); (T.S.); (G.K.D.); (S.A.)
- Correspondence: ; Tel.: +1-403-317-3386
| | - Udaya Subedi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (U.S.); (M.L.); (K.B.H.); (K.K.); (R.O.P.); (T.S.); (G.K.D.); (S.A.)
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (B.S.); (G.C.)
| | - Madeline Lehmann
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (U.S.); (M.L.); (K.B.H.); (K.K.); (R.O.P.); (T.S.); (G.K.D.); (S.A.)
| | - Kimberley Burton Hughes
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (U.S.); (M.L.); (K.B.H.); (K.K.); (R.O.P.); (T.S.); (G.K.D.); (S.A.)
| | - Biruk A. Feyissa
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada; (B.A.F.); (A.H.)
| | - Abdelali Hannoufa
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada; (B.A.F.); (A.H.)
| | - Bin Shan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (B.S.); (G.C.)
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (B.S.); (G.C.)
| | - Kazi Kader
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (U.S.); (M.L.); (K.B.H.); (K.K.); (R.O.P.); (T.S.); (G.K.D.); (S.A.)
| | - Rodrigo Ortega Polo
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (U.S.); (M.L.); (K.B.H.); (K.K.); (R.O.P.); (T.S.); (G.K.D.); (S.A.)
| | - Timothy Schwinghamer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (U.S.); (M.L.); (K.B.H.); (K.K.); (R.O.P.); (T.S.); (G.K.D.); (S.A.)
| | - Gaganpreet Kaur Dhariwal
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (U.S.); (M.L.); (K.B.H.); (K.K.); (R.O.P.); (T.S.); (G.K.D.); (S.A.)
| | - Surya Acharya
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (U.S.); (M.L.); (K.B.H.); (K.K.); (R.O.P.); (T.S.); (G.K.D.); (S.A.)
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Genome-Wide Identification of GRAS Gene Family and Their Responses to Abiotic Stress in Medicago sativa. Int J Mol Sci 2021; 22:ijms22147729. [PMID: 34299352 PMCID: PMC8304046 DOI: 10.3390/ijms22147729] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 02/02/2023] Open
Abstract
Alfalfa (Medicago sativa) is a high-quality legume forage crop worldwide, and alfalfa production is often threatened by abiotic environmental stresses. GRAS proteins are important transcription factors that play a vital role in plant development, as well as in response to environmental stress. In this study, the availability of alfalfa genome "Zhongmu No.1" allowed us to identify 51 GRAS family members, i.e., MsGRAS. MsGRAS proteins could be classified into nine subgroups with distinct conserved domains, and tandem and segmental duplications were observed as an expansion strategy of this gene family. In RNA-Seq analysis, 14 MsGRAS genes were not expressed in the leaf or root, 6 GRAS genes in 3 differentially expressed gene clusters were involved in the salinity stress response in the leaf. Moreover, qRT-PCR results confirmed that MsGRAS51 expression was induced under drought stress and hormone treatments (ABA, GA and IAA) but down-regulated in salinity stress. Collectively, our genome-wide characterization, evolutionary, and expression analysis suggested that the MsGRAS proteins might play crucial roles in response to abiotic stresses and hormonal cues in alfalfa. For the breeding of alfalfa, it provided important information on stress resistance and functional studies on MsGRAS and hormone signaling.
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25
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Identification and Characterization of Abiotic Stress Responsive CBL-CIPK Family Genes in Medicago. Int J Mol Sci 2021; 22:ijms22094634. [PMID: 33924917 PMCID: PMC8124885 DOI: 10.3390/ijms22094634] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) play important roles in plant signal transduction and response to abiotic stress. Plants of Medicago genus contain many important forages, and their growth is often affected by a variety of abiotic stresses. However, studies on the CBL and CIPK family member and their function are rare in Medicago. In this study, a total of 23 CBL and 58 CIPK genes were identified from the genome of Medicago sativa as an important forage crop, and Medicaog truncatula as the model plant. Phylogenetic analysis suggested that these CBL and CIPK genes could be classified into five and seven groups, respectively. Moreover, these genes/proteins showed diverse exon-intron organizations, architectures of conserved protein motifs. Many stress-related cis-acting elements were found in their promoter region. In addition, transcriptional analyses showed that these CBL and CIPK genes exhibited distinct expression patterns in various tissues, and in response to drought, salt, and abscisic acid treatments. In particular, the expression levels of MtCIPK2 (MsCIPK3), MtCIPK17 (MsCIPK11), and MtCIPK18 (MsCIPK12) were significantly increased under PEG, NaCl, and ABA treatments. Collectively, our study suggested that CBL and CIPK genes play crucial roles in response to various abiotic stresses in Medicago.
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Castellani LG, Luchetti A, Nilsson JF, Pérez-Giménez J, Wegener C, Schlüter A, Pühler A, Lagares A, Brom S, Pistorio M, Niehaus K, Torres Tejerizo GA. Exopolysaccharide Characterization of Rhizobium favelukesii LPU83 and Its Role in the Symbiosis With Alfalfa. FRONTIERS IN PLANT SCIENCE 2021; 12:642576. [PMID: 33643369 PMCID: PMC7902896 DOI: 10.3389/fpls.2021.642576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/20/2021] [Indexed: 05/03/2023]
Abstract
One of the greatest inputs of available nitrogen into the biosphere occurs through the biological N2-fixation to ammonium as result of the symbiosis between rhizobia and leguminous plants. These interactions allow increased crop yields on nitrogen-poor soils. Exopolysaccharides (EPS) are key components for the establishment of an effective symbiosis between alfalfa and Ensifer meliloti, as bacteria that lack EPS are unable to infect the host plants. Rhizobium favelukesii LPU83 is an acid-tolerant rhizobia strain capable of nodulating alfalfa but inefficient to fix nitrogen. Aiming to identify the molecular determinants that allow R. favelukesii to infect plants, we studied its EPS biosynthesis. LPU83 produces an EPS I identical to the one present in E. meliloti, but the organization of the genes involved in its synthesis is different. The main gene cluster needed for the synthesis of EPS I in E. meliloti, is split into three different sections in R. favelukesii, which probably arose by a recent event of horizontal gene transfer. A R. favelukesii strain devoided of all the genes needed for the synthesis of EPS I is still able to infect and nodulate alfalfa, suggesting that attention should be directed to other molecules involved in the development of the symbiosis.
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Affiliation(s)
- Lucas G. Castellani
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Abril Luchetti
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Juliet F. Nilsson
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Julieta Pérez-Giménez
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | | | | | | | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Gonzalo A. Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
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Tang Z, Parajuli A, Chen CJ, Hu Y, Revolinski S, Medina CA, Lin S, Zhang Z, Yu LX. Validation of UAV-based alfalfa biomass predictability using photogrammetry with fully automatic plot segmentation. Sci Rep 2021; 11:3336. [PMID: 33558558 PMCID: PMC7870825 DOI: 10.1038/s41598-021-82797-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 01/25/2021] [Indexed: 11/20/2022] Open
Abstract
Alfalfa is the most widely cultivated forage legume, with approximately 30 million hectares planted worldwide. Genetic improvements in alfalfa have been highly successful in developing cultivars with exceptional winter hardiness and disease resistance traits. However, genetic improvements have been limited for complex economically important traits such as biomass. One of the major bottlenecks is the labor-intensive phenotyping burden for biomass selection. In this study, we employed two alfalfa fields to pave a path to overcome the challenge by using UAV images with fully automatic field plot segmentation for high-throughput phenotyping. The first field was used to develop the prediction model and the second field to validate the predictions. The first and second fields had 808 and 1025 plots, respectively. The first field had three harvests with biomass measured in May, July, and September of 2019. The second had one harvest with biomass measured in September of 2019. These two fields were imaged one day before harvesting with a DJI Phantom 4 pro UAV carrying an additional Sentera multispectral camera. Alfalfa plot images were extracted by GRID software to quantify vegetative area based on the Normalized Difference Vegetation Index. The prediction model developed from the first field explained 50-70% (R Square) of biomass variation in the second field by incorporating four features from UAV images: vegetative area, plant height, Normalized Green-Red Difference Index, and Normalized Difference Red Edge Index. This result suggests that UAV-based, high-throughput phenotyping could be used to improve the efficiency of the biomass selection process in alfalfa breeding programs.
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Affiliation(s)
- Zhou Tang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Atit Parajuli
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Chunpeng James Chen
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Yang Hu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Samuel Revolinski
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Cesar Augusto Medina
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, WA, 99350, USA
| | - Sen Lin
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, WA, 99350, USA
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
| | - Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, WA, 99350, USA.
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Li A, Liu A, Du X, Chen JY, Yin M, Hu HY, Shrestha N, Wu SD, Wang HQ, Dou QW, Liu ZP, Liu JQ, Yang YZ, Ren GP. A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa. HORTICULTURE RESEARCH 2020; 7:194. [PMID: 33328470 PMCID: PMC7705661 DOI: 10.1038/s41438-020-00417-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 05/07/2023]
Abstract
Alfalfa (Medicago sativa L.) is one of the most important and widely cultivated forage crops. It is commonly used as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Based on Illumina, Nanopore and Hi-C data, we assembled a chromosome-scale assembly of Medicago sativa spp. caerulea (voucher PI464715), the direct diploid progenitor of autotetraploid alfalfa. The assembled genome comprises 793.2 Mb of genomic sequence and 47,202 annotated protein-coding genes. The contig N50 length is 3.86 Mb. This genome is almost twofold larger and contains more annotated protein-coding genes than that of its close relative, Medicago truncatula (420 Mb and 44,623 genes). The more expanded gene families compared with those in M. truncatula and the expansion of repetitive elements rather than whole-genome duplication (i.e., the two species share the ancestral Papilionoideae whole-genome duplication event) may have contributed to the large genome size of M. sativa spp. caerulea. Comparative and evolutionary analyses revealed that M. sativa spp. caerulea diverged from M. truncatula ~5.2 million years ago, and the chromosomal fissions and fusions detected between the two genomes occurred during the divergence of the two species. In addition, we identified 489 resistance (R) genes and 82 and 85 candidate genes involved in the lignin and cellulose biosynthesis pathways, respectively. The near-complete and accurate diploid alfalfa reference genome obtained herein serves as an important complement to the recently assembled autotetraploid alfalfa genome and will provide valuable genomic resources for investigating the genomic architecture of autotetraploid alfalfa as well as for improving breeding strategies in alfalfa.
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Affiliation(s)
- Ao Li
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ai Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jin-Yuan Chen
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hong-Yin Hu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Sheng-Dan Wu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hai-Qing Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Quan-Wen Dou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Zhi-Peng Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jian-Quan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yong-Zhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.
| | - Guang-Peng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.
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29
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Crain J, Larson S, Dorn K, Hagedorn T, DeHaan L, Poland J. Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3217-3233. [PMID: 32785739 PMCID: PMC7547974 DOI: 10.1007/s00122-020-03666-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/03/2020] [Indexed: 05/28/2023]
Abstract
KEY MESSAGE Paternity assignment and genome-wide association analyses for fertility were applied to a Thinopyrum intermedium breeding program. A lack of progeny between combinations of parents was associated with loci near self-incompatibility genes. In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum intermedium), polycrossing is often used to generate novel recombinants through each cycle of selection, but it cannot track pollen-parent pedigrees and it is unknown how self-incompatibility (SI) genes may limit the number of unique crosses obtained. This study investigated the potential of using next-generation sequencing to assign paternity and identify putative SI loci in IWG. Using a reference population of 380 individuals made from controlled crosses of 64 parents, paternity was assigned with 92% agreement using Cervus software. Using this approach, 80% of 4158 progeny (n = 3342) from a polycross of 89 parents were assigned paternity. Of the 89 pollen parents, 82 (92%) were represented with 1633 unique full-sib families representing 42% of all potential crosses. The number of progeny per successful pollen parent ranged from 1 to 123, with number of inflorescences per pollen parent significantly correlated to the number of progeny (r = 0.54, p < 0.001). Shannon's diversity index, assessing the total number and representation of families, was 7.33 compared to a theoretical maximum of 8.98. To test our hypothesis on the impact of SI genes, a genome-wide association study of the number of progeny observed from the 89 parents identified genetic effects related to non-random mating, including marker loci located near putative SI genes. Paternity testing of polycross progeny can impact future breeding gains by being incorporated in breeding programs to optimize polycross methodology, maintain genetic diversity, and reveal genetic architecture of mating patterns.
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Affiliation(s)
- Jared Crain
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA
| | - Steve Larson
- USDA-ARS, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
| | - Kevin Dorn
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA
- USDA-ARS, Soil Management and Sugarbeet Research, Fort Collins, CO, 80526, USA
| | - Traci Hagedorn
- AAAS Science and Technology Policy Fellow, USDA-APHIS, 4700 River Road, Riverdale, MD, 20737, USA
- Quantitative Scientific Solutions LLC, Arlington, VA, 22203, USA
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, 67401, USA
| | - Jesse Poland
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA.
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, 66506, USA.
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Genetic Diversity among Selected Medicago sativa Cultivars Using Inter-Retrotransposon-Amplified Polymorphism, Chloroplast DNA Barcodes and Morpho-Agronomic Trait Analyses. PLANTS 2020; 9:plants9080995. [PMID: 32764359 PMCID: PMC7464242 DOI: 10.3390/plants9080995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/08/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022]
Abstract
Alfalfa (Medicago sativa L.) is a major forage crop of family Fabaceae and is frequently cultivated in Egypt. The present study is concerned with the genetic discrimination of fifteen alfalfa cultivars from three different countries (Egypt, Australia, and USA) using two molecular approaches: inter-retrotransposon-amplified polymorphism (IRAP) markers and two chloroplast DNA barcodes matK and the trnH in addition to the analysis of fifteen morpho-agronomic traits. The genetic relatedness, based on analysis of IRAP marker polymorphism and produced using eleven primers by clustering via principal component analysis (PCA) and multivariate heatmap biostatistical methods differentiated the two Egyptian cultivars EGY1-Ismailia1 and EGY2-Nubaria1 from the three Australian and seven American cultivars, with some distinction of the cv. USA6-SW9720 and cv. AUS4-SuperFast. The results were also supported by the sequence analysis of the matK and the trnH genes on the genetic relatedness between eight cultivars. Moreover, it might be suggested that breeding lines from M. sativa cultivars may provide novel insights and a better understanding of the domestication of M. sativa genetic diversity. The classification of the eight cultivars, as revealed by morpho-agronomic traits, confirmed the close genetic relationship between the two Egyptian cultivars and indicated some resemblance between them and the AUS2-Siri Nafa, whereas the two American cultivars, USA1-Super supreme and USA4-Cuf101, were clearly isolated from a cluster of other three cultivars USA7-SW9628, USA8-Magna901, and USA9-Perfect. The results are useful sources of genetic information for future breeding programs in crop development and open new possibilities of producing M. sativa lines harboring high forage quality, productivity, and resistance to biotic and abiotic stresses.
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Hrbáčková M, Dvořák P, Takáč T, Tichá M, Luptovčiak I, Šamajová O, Ovečka M, Šamaj J. Biotechnological Perspectives of Omics and Genetic Engineering Methods in Alfalfa. FRONTIERS IN PLANT SCIENCE 2020; 11:592. [PMID: 32508859 PMCID: PMC7253590 DOI: 10.3389/fpls.2020.00592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/20/2020] [Indexed: 05/07/2023]
Abstract
For several decades, researchers are working to develop improved major crops with better adaptability and tolerance to environmental stresses. Forage legumes have been widely spread in the world due to their great ecological and economic values. Abiotic and biotic stresses are main factors limiting legume production, however, alfalfa (Medicago sativa L.) shows relatively high level of tolerance to drought and salt stress. Efforts focused on alfalfa improvements have led to the release of cultivars with new traits of agronomic importance such as high yield, better stress tolerance or forage quality. Alfalfa has very high nutritional value due to its efficient symbiotic association with nitrogen-fixing bacteria, while deep root system can help to prevent soil water loss in dry lands. The use of modern biotechnology tools is challenging in alfalfa since full genome, unlike to its close relative barrel medic (Medicago truncatula Gaertn.), was not released yet. Identification, isolation, and improvement of genes involved in abiotic or biotic stress response significantly contributed to the progress of our understanding how crop plants cope with these environmental challenges. In this review, we provide an overview of the progress that has been made in high-throughput sequencing, characterization of genes for abiotic or biotic stress tolerance, gene editing, as well as proteomic and metabolomics techniques bearing biotechnological potential for alfalfa improvement.
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Affiliation(s)
| | | | | | | | | | | | | | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
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Chen H, Zeng Y, Yang Y, Huang L, Tang B, Zhang H, Hao F, Liu W, Li Y, Liu Y, Zhang X, Zhang R, Zhang Y, Li Y, Wang K, He H, Wang Z, Fan G, Yang H, Bao A, Shang Z, Chen J, Wang W, Qiu Q. Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa. Nat Commun 2020; 11:2494. [PMID: 32427850 PMCID: PMC7237683 DOI: 10.1038/s41467-020-16338-x] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 04/28/2020] [Indexed: 02/07/2023] Open
Abstract
Artificially improving traits of cultivated alfalfa (Medicago sativa L.), one of the most important forage crops, is challenging due to the lack of a reference genome and an efficient genome editing protocol, which mainly result from its autotetraploidy and self-incompatibility. Here, we generate an allele-aware chromosome-level genome assembly for the cultivated alfalfa consisting of 32 allelic chromosomes by integrating high-fidelity single-molecule sequencing and Hi-C data. We further establish an efficient CRISPR/Cas9-based genome editing protocol on the basis of this genome assembly and precisely introduce tetra-allelic mutations into null mutants that display obvious phenotype changes. The mutated alleles and phenotypes of null mutants can be stably inherited in generations in a transgene-free manner by cross pollination, which may help in bypassing the debate about transgenic plants. The presented genome and CRISPR/Cas9-based transgene-free genome editing protocol provide key foundations for accelerating research and molecular breeding of this important forage crop.
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Affiliation(s)
- Haitao Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Guangdong Sanjie Forage Biotechnology Co., Ltd., 510630, Guangzhou, China
- Sanjie Institute of Forage, 712100, Yangling, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 650204, Kunming, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yan Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 650204, Kunming, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Lanzhou University, 730000, Lanzhou, China
| | - Lingli Huang
- Guangdong Sanjie Forage Biotechnology Co., Ltd., 510630, Guangzhou, China
- Sanjie Institute of Forage, 712100, Yangling, China
- School of Ecology and Environment, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Bolin Tang
- Guangdong Sanjie Forage Biotechnology Co., Ltd., 510630, Guangzhou, China
- Sanjie Institute of Forage, 712100, Yangling, China
- State Key Laboratory of Grassland Agro-Ecosystem, Lanzhou University, 730000, Lanzhou, China
| | - He Zhang
- BGI-Qingdao, 266555, Qingdao, China
| | - Fei Hao
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Wei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Guangdong Sanjie Forage Biotechnology Co., Ltd., 510630, Guangzhou, China
- Sanjie Institute of Forage, 712100, Yangling, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 650204, Kunming, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Youhan Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, 650223, Kunming, China
| | - Yanbin Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Lanzhou University, 730000, Lanzhou, China
| | - Xiaoshuang Zhang
- Guangdong Sanjie Forage Biotechnology Co., Ltd., 510630, Guangzhou, China
- Sanjie Institute of Forage, 712100, Yangling, China
| | - Ru Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Yesheng Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
| | - Yongxin Li
- School of Ecology and Environment, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Hua He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, 650223, Kunming, China
| | - Zhongkai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, 710072, Xi'an, China
| | | | - Hui Yang
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Aike Bao
- State Key Laboratory of Grassland Agro-Ecosystem, Lanzhou University, 730000, Lanzhou, China
| | - Zhanhuan Shang
- State Key Laboratory of Grassland Agro-Ecosystem, Lanzhou University, 730000, Lanzhou, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, 650223, Kunming, China.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.
- School of Ecology and Environment, Northwestern Polytechnical University, 710072, Xi'an, China.
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, 710072, Xi'an, China.
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Wang Z, Wang X, Zhang H, Ma L, Zhao H, Jones CS, Chen J, Liu G. A genome-wide association study approach to the identification of candidate genes underlying agronomic traits in alfalfa (Medicago sativa L.). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:611-613. [PMID: 31487419 PMCID: PMC7004897 DOI: 10.1111/pbi.13251] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/26/2019] [Accepted: 08/29/2019] [Indexed: 05/04/2023]
Affiliation(s)
- Zan Wang
- Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xuemin Wang
- Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Han Zhang
- Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Lin Ma
- Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Haiming Zhao
- Institute of Dry FarmingHebei Academy of Agriculture and Forestry SciencesHengshuiChina
| | | | - Jin Chen
- Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Guibo Liu
- Institute of Dry FarmingHebei Academy of Agriculture and Forestry SciencesHengshuiChina
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Jiang P, Shao J, Nemchinov LG. Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.). Virol J 2019; 16:153. [PMID: 31818304 PMCID: PMC6902351 DOI: 10.1186/s12985-019-1257-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Publicly available transcriptomic datasets have become a valuable tool for the discovery of new pathogens, particularly viruses. In this study, several coding-complete viral genomes previously not found or experimentally confirmed in alfalfa were identified in the plant datasets retrieved from the NCBI Sequence Read Archive. METHODS Publicly available Medicago spp. transcriptomic datasets were retrieved from the NCBI SRA database. The raw reads were first mapped to the reference genomes of Medicago sativa and Medigago truncatula followed by the alignment of the unmapped reads to the NCBI viral genome database and de novo assembly using the SPAdes tool. When possible, assemblies were experimentally confirmed using 5'/3' RACE and RT-PCRs. RESULTS Twenty three different viruses were identified in the analyzed datasets, of which several represented emerging viruses not reported in alfalfa prior to this study. Among them were two strains of cnidium vein yellowing virus, lychnis mottle virus and Cactus virus X, for which coding-complete genomic sequences were obtained by a de novo assembly. CONCLUSIONS The results improve our knowledge of the diversity and host range of viruses infecting alfalfa, provide essential tools for their diagnostics and characterization and demonstrate the utility of transcriptomic datasets for the discovery of new pathogens.
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Affiliation(s)
- Peng Jiang
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA
| | - Jonathan Shao
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA
| | - Lev G Nemchinov
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA.
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Lei Y, Hannoufa A, Wang Y, Christensen D, Yu P. Effects of silencing TT8 and HB12 on in vitro nutrients degradation and VFA production in relation to molecular structures of alfalfa (Medicago sativa). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:6850-6858. [PMID: 31385316 DOI: 10.1002/jsfa.9970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/13/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Transparent Testa8 (TT8) and Homeobox12 (HB12) are two transcriptional factors in plant phenylpropanoid pathways and were reported to be positively related to lignin content. Alfalfa with silenced TT8 (TT8i) and HB12 (HB12i) was therefore generated using the RNA interference (RNAi) technique. Although lignin was found to be high in HB12i, such gene-silencing of alfalfa resulted in nutrient profiles that might be suitable for grazing. To extend the nutritional evaluation of transformed alfalfa, ground samples of 11 HB12i, 5 TT8i and 4 wild type (WT) were incubated in rumen fluid : buffer solution for 0, 2, 4, 8, 12, 24 and 48 h at 39 °C. Dry matter (DM) and neutral detergent fiber (NDF) degradations at each time point, and production of volatile fatty acids (VFA) at 4, 12, 24 and 48 h were analyzed, as well as degradation and production kinetics. The correlations and regressions between nutritive profiles and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectral parameters were determined. RESULTS Both transformed genotypes had lower DM degradation and HB12i had lower VFA production compared with WT. Structural carbohydrate (STC) parameters were found to be negatively correlated with DM degradation and VFA production. The kinetics of DM degradation and VFA production were predicted from spectral parameters with good estimation power. CONCLUSION Silencing of HB12 and TT8 affected fermentation characteristics of alfalfa and some fermentation characteristics were predictable from spectral parameters using ATR-FTIR spectroscopy. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Yaogeng Lei
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Abdelali Hannoufa
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Yuxi Wang
- Agriculture and Agri-Food, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - David Christensen
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Peiqiang Yu
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Joshi DC, Chaudhari GV, Sood S, Kant L, Pattanayak A, Zhang K, Fan Y, Janovská D, Meglič V, Zhou M. Revisiting the versatile buckwheat: reinvigorating genetic gains through integrated breeding and genomics approach. PLANTA 2019; 250:783-801. [PMID: 30623242 DOI: 10.1007/s00425-018-03080-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/20/2018] [Indexed: 05/09/2023]
Abstract
Emerging insights in buckwheat molecular genetics allow the integration of genomics driven breeding to revive this ancient crop of immense nutraceutical potential from Asia. Out of several thousand known edible plant species, only four crops-rice, wheat, maize and potato provide the largest proportion of daily nutrition to billions of people. While these crops are the primary supplier of carbohydrates, they lack essential amino acids and minerals for a balanced nutrition. The overdependence on only few crops makes the future cropping systems vulnerable to the predicted climate change. Diversifying food resources through incorporation of orphan or minor crops in modern cropping systems is one potential strategy to improve the nutritional security and mitigate the hostile weather patterns. One such crop is buckwheat, which can contribute to the agricultural sustainability as it grows in a wide range of environments, requires relatively low inputs and possess balanced amino acid and micronutrient profiles. Additionally, gluten-free nature of protein and nutraceutical properties of secondary metabolites make the crop a healthy alternative of wheat-based diet in developed countries. Despite enormous potential, efforts for the genetic improvement of buckwheat are considerably lagged behind the conventional cereal crops. With the draft genome sequences in hand, there is a great scope to speed up the progress of genetic improvement of buckwheat. This article outlines the state of the art in buckwheat research and provides concrete perspectives how modern breeding approaches can be implemented to accelerate the genetic gain. Our suggestions are transferable to many minor and underutilized crops to address the issue of limited genetic gain and low productivity.
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Affiliation(s)
- D C Joshi
- Indian Council of Agricultural Research-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, India.
| | - Ganesh V Chaudhari
- Indian Council of Agricultural Research-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, India
| | - Salej Sood
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Lakshmi Kant
- Indian Council of Agricultural Research-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, India
| | - A Pattanayak
- Indian Council of Agricultural Research-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, India
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dagmar Janovská
- Department of Gene Bank, Crop Research Institute, Drnovská, Prague, Czech Republic
| | - Vladimir Meglič
- Agricultural Institute of Slovenia, Hacquetova ulica, Ljubljana, Slovenia
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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Lorenzo CD, Alonso Iserte J, Sanchez Lamas M, Antonietti MS, Garcia Gagliardi P, Hernando CE, Dezar CAA, Vazquez M, Casal JJ, Yanovsky MJ, Cerdán PD. Shade delays flowering in Medicago sativa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:7-22. [PMID: 30924988 DOI: 10.1111/tpj.14333] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/01/2019] [Accepted: 03/25/2019] [Indexed: 05/13/2023]
Abstract
Shade-intolerant plants respond to the decrease in the red (R) to far-red (FR) light ratio (R:FR) occurring under shade by elongating stems and petioles and by re-positioning leaves, in a race to outcompete neighbors for the sunlight resource. In some annual species, the shade avoidance syndrome (SAS) is accompanied by the early induction of flowering. Anticipated flowering is viewed as a strategy to set seeds before the resources become severely limiting. Little is known about the molecular mechanisms of SAS in perennial forage crops like alfalfa (Medicago sativa). To study SAS in alfalfa, we exposed alfalfa plants to simulated shade by supplementing with FR light. Low R:FR light produced a classical SAS, with increased internode and petiole lengths, but unexpectedly also with delayed flowering. To understand the molecular mechanisms involved in uncoupling SAS from early flowering, we used a transcriptomic approach. The SAS is likely to be mediated by increased expression of msPIF3 and msHB2 in low R:FR light. Constitutive expression of these genes in Arabidopsis led to SAS, including early flowering, strongly suggesting that their roles are conserved. Delayed flowering was likely to be mediated by the downregulation of msSPL3, which promotes flowering in both Arabidopsis and alfalfa. Shade-delayed flowering in alfalfa may be important to extend the vegetative phase under suboptimal light conditions, and thus assure the accumulation of reserves necessary to resume growth after the next season.
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Affiliation(s)
- Christian D Lorenzo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWE, Buenos Aires, Argentina
| | - Javier Alonso Iserte
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWE, Buenos Aires, Argentina
| | - Maximiliano Sanchez Lamas
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWE, Buenos Aires, Argentina
| | - Mariana Sofia Antonietti
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWE, Buenos Aires, Argentina
| | - Pedro Garcia Gagliardi
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWE, Buenos Aires, Argentina
| | - Carlos E Hernando
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWE, Buenos Aires, Argentina
| | - Carlos Alberto A Dezar
- Instituto de Agrobiotecnología de Rosario (INDEAR), CONICET, S2000EZP, Rosario, Argentina
| | - Martin Vazquez
- Instituto de Agrobiotecnología de Rosario (INDEAR), CONICET, S2000EZP, Rosario, Argentina
| | - Jorge J Casal
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWE, Buenos Aires, Argentina
- Instituto de Fisiología vegetal, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWE, Buenos Aires, Argentina
| | - Pablo D Cerdán
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWE, Buenos Aires, Argentina
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Zhang F, Kang J, Long R, Yu LX, Wang Z, Zhao Z, Zhang T, Yang Q. High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq. BMC PLANT BIOLOGY 2019; 19:165. [PMID: 31029106 PMCID: PMC6487053 DOI: 10.1186/s12870-019-1770-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 04/10/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Alfalfa (Medicago sativa L.) is an important forage crop grown worldwide. Alfalfa is called the "queen of forage crops" due to its high forage yield and nutritional characteristics. The aim of this study was to undertake quantitative trait loci (QTL) mapping of yield and yield-related traits in an F1 population of two alfalfa varieties that differ in their yield and yield-related traits. RESULTS We constructed a high-density linkage map using single nucleotide polymorphism (SNP) markers generated by restriction-site associated DNA sequencing (RAD-seq). The linkage map contains 4346 SNP and 119 simple sequence repeat (SSR) markers, with 32 linkage groups for each parent. The average marker distances were 3.00 and 1.32 cM, with coverages of 3455 cM and 4381 cM for paternal and maternal linkage maps, respectively. Using these maps and phenotypic data, we identified a total of 21 QTL for yield and yield components, including five for yield, five for plant height, five for branch number, and six for shoot diameter. Among them, six QTL were co-located for more than one trait. Five QTL explained more than 10% of the phenotypic variation. CONCLUSIONS We used RAD-seq to construct a linkage map for alfalfa that greatly enhanced marker density compared to previous studies. This high-density linkage map of alfalfa is a useful reference for mapping yield-related traits. Identified yield-related loci could be used to validate their usefulness in developing markers for maker-assisted selection in breeding populations to improve yield potential in alfalfa.
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Affiliation(s)
- Fan Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junmei Kang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long-Xi Yu
- Plant Germplasm Introduction and Testing Research, United States Department of Agriculture-Agricultural Research Service, Prosser, WA, USA
| | - Zhen Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhongxiang Zhao
- Cangzhou Technical College and Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Tiejun Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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Liu XP, Hawkins C, Peel MD, Yu LX. Genetic Loci Associated with Salt Tolerance in Advanced Breeding Populations of Tetraploid Alfalfa Using Genome-Wide Association Studies. THE PLANT GENOME 2019; 12:180026. [PMID: 30951087 DOI: 10.3835/plantgenome2018.05.0026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Many agricultural lands in the western United States consist of soil with high concentrations of salt, which is detrimental to alfalfa ( L.) growth and production, especially in the region where water resource is limited. Developing alfalfa varieties with salt tolerance is imperative for sustainable production under increasing soil salinity. In the present study, we used advanced alfalfa breeding populations and evaluated five traits related to salt tolerance including biomass dry weight (DW) and fresh weight (FW), plant height (PH), leaf relative water content (RWC), and stomatal conductance (SC) under control and salt stress. Stress susceptibility index (SSI) of each trait and single-nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS) were used for genome-wide association studies (GWAS) to identify loci associated with salt tolerance. A total of 53 significant SNPs associated with salt tolerance were identified and they were located at 49 loci through eight chromosomes. A Basic Local Alignment Search Tool (BLAST) search of the regions surrounding the SNPs revealed 21 putative candidate genes associated with salt tolerance. The genetic architecture for traits related to salt tolerance characterized in this report could help in understanding the genetic mechanism by which salt stress affects plant growth and production in alfalfa. The markers and candidate genes identified in the present study would be useful for marker-assisted selection (MAS) in breeding salt-tolerant alfalfa after validation of the markers.
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Mousavi‐Derazmahalleh M, Bayer PE, Hane JK, Valliyodan B, Nguyen HT, Nelson MN, Erskine W, Varshney RK, Papa R, Edwards D. Adapting legume crops to climate change using genomic approaches. PLANT, CELL & ENVIRONMENT 2019; 42:6-19. [PMID: 29603775 PMCID: PMC6334278 DOI: 10.1111/pce.13203] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/10/2018] [Indexed: 05/05/2023]
Abstract
Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.
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Affiliation(s)
- Mahsa Mousavi‐Derazmahalleh
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - Philipp E. Bayer
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - James K. Hane
- CCDM BioinformaticsCentre for Crop Disease Management, Curtin UniversityBentleyWestern Australia6102Australia
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Matthew N. Nelson
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Natural Capital and Plant HealthRoyal Botanic Gardens Kew, Wakehurst PlaceArdinglyWest SussexRH17 6TNUK
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - William Erskine
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Centre for Plant Genetics and BreedingThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - Rajeev K. Varshney
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Patancheru502 324India
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - David Edwards
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
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41
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Hawkins C, Yu LX. Recent progress in alfalfa (Medicago sativa L.) genomics and genomic selection. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.cj.2018.01.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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42
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Xiong X, Liu N, Wei YQ, Bi YX, Luo JC, Xu RX, Zhou JQ, Zhang YJ. Effects of non-uniform root zone salinity on growth, ion regulation, and antioxidant defense system in two alfalfa cultivars. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:434-444. [PMID: 30290335 DOI: 10.1016/j.plaphy.2018.09.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/31/2018] [Accepted: 09/20/2018] [Indexed: 06/08/2023]
Abstract
A split-root system was established to investigate the effects of uniform (0/0, 50/50, and 200/200 mM salt [NaCl]) and non-uniform (0/200 and 50/200 mM NaCl) salt stress on growth, ion regulation, and the antioxidant defense system of alfalfa (Medicago sativa) by comparing a salt-tolerant (Zhongmu No.1) and salt-sensitive (Algonquin) cultivar. We found that non-uniform salinity was associated with greater plant growth rate and shoot dry weight, lower leaf Na+ concentration, higher leaf potassium cation (K+) concentration, lower lipid peroxidation, and greater superoxide dismutase (EC 1.15.1.1), catalase (EC 1.11.1.6), and peroxidase (EC 1.11.1.7) activities, compared to uniform salt stress in both alfalfa cultivars. Under non-uniform salinity, a significant increase in Na+ concentration and Na+ efflux and a decline in K+ efflux in the no-saline or low-saline part of the roots alleviated salt damage. Our results also demonstrated that proline and antioxidant enzymes accumulated in both the no- or low-saline and high-saline roots, revealing that osmotic adjustment and antioxidant defense had systemic rather than localized effects in alfalfa plants, and there was a functional equilibrium within the root system under non-uniform salt stress. The salt-tolerant cultivar Zhongmu No.1 exhibited greater levels of growth compared to Algonquin under both uniform and non-uniform salt stress, with Na+ tolerance and efflux abilities more effective and greater antioxidant defense capacity evident for cultivar Zhongmu No.1.
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Affiliation(s)
- Xue Xiong
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China; Hebei Normal University for Nationalities, Chengde, 067000, China
| | - Nan Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China
| | - Yu-Qi Wei
- College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China
| | - Yi-Xian Bi
- College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China
| | - Jian-Chuan Luo
- Institute of Grassland Research of CAAS, Huhhot, 010010, China
| | - Rui-Xuan Xu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China
| | - Ji-Qiong Zhou
- Department of Grassland Science, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ying-Jun Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China; College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China; Key Laboratory of Grasslands Management and Utilization, Ministry of Agriculture, Beijing, 100094, China.
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Kulkarni KP, Tayade R, Asekova S, Song JT, Shannon JG, Lee JD. Harnessing the Potential of Forage Legumes, Alfalfa, Soybean, and Cowpea for Sustainable Agriculture and Global Food Security. FRONTIERS IN PLANT SCIENCE 2018; 9:1314. [PMID: 30283466 PMCID: PMC6157451 DOI: 10.3389/fpls.2018.01314] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/20/2018] [Indexed: 05/18/2023]
Abstract
Substantial improvements in access to food and increased purchasing power are driving many people toward consuming nutrition-rich foods causing an unprecedented demand for protein food worldwide, which is expected to rise further. Forage legumes form an important source of feed for livestock and have potential to provide a sustainable solution for food and protein security. Currently, alfalfa is a commercially grown source of forage and feed in many countries. However, soybean and cowpea also have the potential to provide quality forage and fodder for animal use. The cultivation of forage legumes is under threat from changing climatic conditions, indicating the need for breeding cultivars that can sustain and acclimatize to the negative effects of climate change. Recent progress in genetic and genomic tools have facilitated the identification of quantitative trait loci and genes/alleles that can aid in developing forage cultivars through genomics-assisted breeding. Furthermore, transgenic technology can be utilized to manipulate the genetic makeup of plants to improve forage digestibility for better animal performance. In this article, we assess the genetic potential of three important legume crops, alfalfa, soybean, and cowpea in supplying quality fodder and feed for livestock. In addition, we examine the impact of climate change on forage quality and discuss efforts made in enhancing the adaptation of the plant to the abiotic stress conditions. Subsequently, we suggest the application of integrative approaches to achieve adequate forage production amid the unpredictable climatic conditions.
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Affiliation(s)
| | - Rupesh Tayade
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Sovetgul Asekova
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, South Korea
| | - Jong Tae Song
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - J. Grover Shannon
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Jeong-Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
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Nemchinov LG, François S, Roumagnac P, Ogliastro M, Hammond RW, Mollov DS, Filloux D. Characterization of alfalfa virus F, a new member of the genus Marafivirus. PLoS One 2018; 13:e0203477. [PMID: 30180217 PMCID: PMC6122807 DOI: 10.1371/journal.pone.0203477] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/21/2018] [Indexed: 01/27/2023] Open
Abstract
Viral infections of alfalfa are widespread in major cultivation areas and their impact on alfalfa production may be underestimated. A new viral species, provisionally named alfalfa virus F (AVF), was identified using a virion-associated nucleic acid (VANA) metagenomics-based approach in alfalfa (Medicago sativa L.) samples collected in Southern France. The nucleotide sequence of the viral genome was determined by de-novo assembly of VANA reads and by 5'/3' RACE with viral RNA extracted from enriched viral particles or with total RNA, respectively. The virus shares the greatest degree of overall sequence identity (~78%) with Medicago sativa marafivirus 1 (MsMV1) recently deduced from alfalfa transcriptomic data. The tentative nucleotide sequence of the AVF coat protein shares ~83% identity with the corresponding region of MsMV1. A sequence search of the predicted single large ORF encoding a polyprotein of 235kDa in the Pfam database resulted in identification of five domains, characteristic of the genus Marafivirus, family Tymoviridae. The AVF genome also contains a conserved "marafibox", a 16-nt consensus sequence present in all known marafiviruses. Phylogenetic analysis of the complete nucleotide sequences of AVF and other viruses of the family Tymoviridae grouped AVF in the same cluster with MsMV1. In addition to 5' and 3' terminal extensions, the identity of the virus was confirmed by RT-PCRs with primers derived from VANA-contigs, transmission electron microscopy with virus-infected tissues and transient expression of the viral coat protein gene using a heterologous virus-based vector. Based on the criteria demarcating species in the genus Marafivirus that include overall sequence identity less than 80% and coat protein identity less than 90%, we propose that AVF represents a distinct viral species in the genus Marafivirus, family Tymoviridae.
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Affiliation(s)
- Lev G. Nemchinov
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville MD, United States of America
| | | | - Phillipe Roumagnac
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier
| | | | - Rosemarie W. Hammond
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville MD, United States of America
| | - Dimitre S. Mollov
- USDA-ARS, National Germplasm Recourses Laboratory, Beltsville MD, United States of America
| | - Denis Filloux
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier
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Adhikari L, Lindstrom OM, Markham J, Missaoui AM. Dissecting Key Adaptation Traits in the Polyploid Perennial Medicago sativa Using GBS-SNP Mapping. FRONTIERS IN PLANT SCIENCE 2018; 9:934. [PMID: 30022989 PMCID: PMC6039623 DOI: 10.3389/fpls.2018.00934] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/11/2018] [Indexed: 05/18/2023]
Abstract
Understanding key adaptation traits is crucial to developing new cultivars with broad adaptations. The main objective of this research is to understand the genetic basis of winter hardiness (WH) and fall dormancy (FD) in alfalfa and the association between the two traits. QTL analysis was conducted in a pseudo-testcross F1 population developed from two cultivars contrasting in FD (3010 with FD = 2 and CW 1010 with FD = 10). The mapping population was evaluated in three replications at two locations (Watkinsville and Blairsville, GA). FD levels showed low to moderate correlations with WH (0.22-0.57). Assessing dormancy in winter is more reliable than in the fall in southern regions with warm winters. The mapping population was genotyped using Genotyping-by-sequencing (GBS). Single dose allele SNPs (SDA) were used for constructing linkage maps. The parental map (CW 1010) consisted of 32 linkage groups spanning 2127.5 cM with 1377 markers and an average marker density of 1.5 cM/SNP. The maternal map (3010) had 32 linkage groups spanning 2788.4 cM with 1837 SDA SNPs with an average marker density of 1.5 cM/SNP. Forty-five significant (P < 0.05) QTLs for FD and 35 QTLs for WH were detected on both male and female linkage maps. More than 75% (22/28) of the dormancy QTL detected from the 3010 parent did not share genomic regions with WH QTLs and more than 70% (12/17) dormancy QTLs detected from CW 1010 parent were localized in different genomic regions than WH QTLs. These results suggest that the two traits have independent inheritance and therefore can be improved separately in breeding programs.
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Affiliation(s)
- Laxman Adhikari
- Crop and Soil Sciences and Institute of Plant Breeding Genetics and Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | | | - Jonathan Markham
- Crop and Soil Sciences and Institute of Plant Breeding Genetics and Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Ali M. Missaoui
- Crop and Soil Sciences and Institute of Plant Breeding Genetics and Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
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Gao R, Gruber MY, Amyot L, Hannoufa A. SPL13 regulates shoot branching and flowering time in Medicago sativa. PLANT MOLECULAR BIOLOGY 2018; 96:119-133. [PMID: 29149417 DOI: 10.1007/s11103-017-0683-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/10/2017] [Indexed: 05/20/2023]
Abstract
Our results show SPL13 plays a crucial role in regulating vegetative and reproductive development in Medicago sativa L. (alfalfa), and that MYB112 is targeted and downregulated by SPL13 in alfalfa. We previously showed that transgenic Medicago sativa (alfalfa) plants overexpressing microRNA156 (miR156) show a bushy phenotype, reduced internodal length, delayed flowering time, and enhanced biomass yield. In alfalfa, transcripts of seven SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, including SPL13, are targeted for cleavage by miR156. Thus, association of each target SPL gene to a trait or set of traits is essential for developing molecular markers for alfalfa breeding. In this study, we investigated SPL13 function using SPL13 overexpression and silenced alfalfa plants. Severe growth retardation, distorted branches and up-curled leaves were observed in miR156-impervious 35S::SPL13m over-expression plants. In contrast, more lateral branches and delayed flowering time were observed in SPL13 silenced plants. SPL13 transcripts were predominantly present in the plant meristems, indicating that SPL13 is involved in regulating shoot branch development. Accordingly, the shoot branching-related CAROTENOID CLEAVAGE DIOXYGENASE 8 gene was found to be significantly downregulated in SPL13 RNAi silencing plants. A R2R3-MYB gene MYB112 was also identified as being directly silenced by SPL13 based on Next Generation Sequencing-mediated transcriptome analysis and chromatin immunoprecipitation assays, suggesting that MYB112 may be involved in regulating alfalfa vegetative growth.
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Affiliation(s)
- Ruimin Gao
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Margaret Y Gruber
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Lisa Amyot
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.
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47
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Nemchinov LG, Grinstead SC, Mollov DS. Alfalfa virus S, a new species in the family Alphaflexiviridae. PLoS One 2017; 12:e0178222. [PMID: 28558046 PMCID: PMC5448757 DOI: 10.1371/journal.pone.0178222] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/10/2017] [Indexed: 12/14/2022] Open
Abstract
A new species of the family Alphaflexiviridae provisionally named alfalfa virus S (AVS) was discovered in alfalfa samples originating from Sudan. A complete nucleotide sequence of the viral genome consisting of 8,349 nucleotides excluding the 3' poly(A) tail was determined by high throughput sequencing (HTS) on an Illumina platform. NCBI BLAST searches revealed that the virus shares the greatest degree of sequence identity with members of the family Alphaflexiviridae, genus Allexivirus. The AVS genome contains six computationally-predicted open reading frames (ORF) encoding viral replication protein, triple gene block protein 1 (TGB1), TGB2, TGB3-like protein, unknown 38.4 kDa protein resembling serine-rich 40 kDa protein characteristic for allexiviruses, and coat protein (CP). AVS lacks a clear 3' proximal ORF that encodes a nucleic acid-binding protein typical for allexiviruses. The identity of the virus was confirmed by RT-PCR with primers derived from the HTS-generated sequence, dot blot hybridization with DIG-labeled virus-specific RNA probes, and Western blot analysis with antibodies produced against a peptide derived from the CP sequence. Transmission electron microscopic observations of the infected tissues showed the presence of filamentous particles similar to allexiviruses in their length and appearance. To the best of our knowledge, this is the first report on the identification of a putative allexivirus in alfalfa (Medicago sativa). The genome sequence of AVS has been deposited in NCBI GenBank on 03/02/2016 as accession № KY696659.
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Affiliation(s)
- Lev G. Nemchinov
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Samuel C. Grinstead
- USDA-ARS, National Germplasm Recourses Laboratory, Beltsville, Maryland, United States of America
| | - Dimitre S. Mollov
- USDA-ARS, National Germplasm Recourses Laboratory, Beltsville, Maryland, United States of America
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Yu L, Zheng P, Zhang T, Rodringuez J, Main D. Genotyping-by-sequencing-based genome-wide association studies on Verticillium wilt resistance in autotetraploid alfalfa (Medicago sativa L.). MOLECULAR PLANT PATHOLOGY 2017; 18:187-194. [PMID: 26933934 PMCID: PMC6638244 DOI: 10.1111/mpp.12389] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Verticillium wilt (VW) is a fungal disease that causes severe yield losses in alfalfa. The most effective method to control the disease is through the development and use of resistant varieties. The identification of marker loci linked to VW resistance can facilitate breeding for disease-resistant alfalfa. In the present investigation, we applied an integrated framework of genome-wide association with genotyping-by-sequencing (GBS) to identify VW resistance loci in a panel of elite alfalfa breeding lines. Phenotyping was performed by manual inoculation of the pathogen to healthy seedlings, and scoring for disease resistance was carried out according to the standard test of the North America Alfalfa Improvement Conference (NAAIC). Marker-trait association by linkage disequilibrium identified 10 single nucleotide polymorphism (SNP) markers significantly associated with VW resistance. Alignment of the SNP marker sequences to the M. truncatula genome revealed multiple quantitative trait loci (QTLs). Three, two, one and five markers were located on chromosomes 5, 6, 7 and 8, respectively. Resistance loci found on chromosomes 7 and 8 in the present study co-localized with the QTLs reported previously. A pairwise alignment (blastn) using the flanking sequences of the resistance loci against the M. truncatula genome identified potential candidate genes with putative disease resistance function. With further investigation, these markers may be implemented into breeding programmes using marker-assisted selection, ultimately leading to improved VW resistance in alfalfa.
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Affiliation(s)
- Long‐Xi Yu
- United States Department of Agriculture‐Agricultural Research ServicePlant Germplasm Introduction and Testing Research24106 N Bunn RoadProsserWA99350 USA
| | - Ping Zheng
- Department of HorticultureWashington State UniversityPullmanWA99164 USA
| | - Tiejun Zhang
- United States Department of Agriculture‐Agricultural Research ServicePlant Germplasm Introduction and Testing Research24106 N Bunn RoadProsserWA99350 USA
- Present address:
Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijing100193 China
| | - Jonas Rodringuez
- Forage Genetics International, Inc.7661 Becker RoadDavisCA95618 USA
| | - Dorrie Main
- Department of HorticultureWashington State UniversityPullmanWA99164 USA
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Biazzi E, Nazzicari N, Pecetti L, Brummer EC, Palmonari A, Tava A, Annicchiarico P. Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits. PLoS One 2017; 12:e0169234. [PMID: 28068350 PMCID: PMC5222375 DOI: 10.1371/journal.pone.0169234] [Citation(s) in RCA: 56] [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: 09/26/2016] [Accepted: 12/13/2016] [Indexed: 12/03/2022] Open
Abstract
Genetic progress for forage quality has been poor in alfalfa (Medicago sativa L.), the most-grown forage legume worldwide. This study aimed at exploring opportunities for marker-assisted selection (MAS) and genomic selection of forage quality traits based on breeding values of parent plants. Some 154 genotypes from a broadly-based reference population were genotyped by genotyping-by-sequencing (GBS), and phenotyped for leaf-to-stem ratio, leaf and stem contents of protein, neutral detergent fiber (NDF) and acid detergent lignin (ADL), and leaf and stem NDF digestibility after 24 hours (NDFD), of their dense-planted half-sib progenies in three growing conditions (summer harvest, full irrigation; summer harvest, suspended irrigation; autumn harvest). Trait-marker analyses were performed on progeny values averaged over conditions, owing to modest germplasm × condition interaction. Genomic selection exploited 11,450 polymorphic SNP markers, whereas a subset of 8,494 M. truncatula-aligned markers were used for a genome-wide association study (GWAS). GWAS confirmed the polygenic control of quality traits and, in agreement with phenotypic correlations, indicated substantially different genetic control of a given trait in stems and leaves. It detected several SNPs in different annotated genes that were highly linked to stem protein content. Also, it identified a small genomic region on chromosome 8 with high concentration of annotated genes associated with leaf ADL, including one gene probably involved in the lignin pathway. Three genomic selection models, i.e., Ridge-regression BLUP, Bayes B and Bayesian Lasso, displayed similar prediction accuracy, whereas SVR-lin was less accurate. Accuracy values were moderate (0.3-0.4) for stem NDFD and leaf protein content, modest for leaf ADL and NDFD, and low to very low for the other traits. Along with previous results for the same germplasm set, this study indicates that GBS data can be exploited to improve both quality traits (by genomic selection or MAS) and forage yield.
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Affiliation(s)
- Elisa Biazzi
- Council for Agricultural Research and Economics—Research Centre for Fodder Crops and Dairy Productions (CREA-FLC), Lodi, Italy
| | - Nelson Nazzicari
- Council for Agricultural Research and Economics—Research Centre for Fodder Crops and Dairy Productions (CREA-FLC), Lodi, Italy
| | - Luciano Pecetti
- Council for Agricultural Research and Economics—Research Centre for Fodder Crops and Dairy Productions (CREA-FLC), Lodi, Italy
| | - E. Charles Brummer
- Plant Breeding Center, Department of Plant Sciences, University of California, Davis, CA, United States of America
| | - Alberto Palmonari
- Department of Veterinary Medicine, University of Bologna, Bologna, Italy
| | - Aldo Tava
- Council for Agricultural Research and Economics—Research Centre for Fodder Crops and Dairy Productions (CREA-FLC), Lodi, Italy
| | - Paolo Annicchiarico
- Council for Agricultural Research and Economics—Research Centre for Fodder Crops and Dairy Productions (CREA-FLC), Lodi, Italy
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50
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Gao R, Austin RS, Amyot L, Hannoufa A. Comparative transcriptome investigation of global gene expression changes caused by miR156 overexpression in Medicago sativa. BMC Genomics 2016; 17:658. [PMID: 27542359 PMCID: PMC4992203 DOI: 10.1186/s12864-016-3014-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/12/2016] [Indexed: 11/24/2022] Open
Abstract
Background Medicago sativa (alfalfa) is a low-input forage and potential bioenergy crop, and improving its yield and quality has always been a focus of the alfalfa breeding industry. Transgenic alfalfa plants overexpressing a precursor of alfalfa microRNA156 (MsmiR156) were recently generated by our group. These plants (miR156OE) showed enhanced biomass yield, reduced internodal length, increased shoot branching and trichome density, and a delay in flowering time. Transcripts of three SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes (MsSPL6, MsSPL12, and MsSPL13) were found to be targeted for cleavage by MsmiR156 in alfalfa. Results To further illustrate the molecular mechanisms underlying the effects of miR156 in alfalfa, two miR156OE genotypes (A11a and A17) were subjected to Next Generation RNA Sequencing with Illumina HiSeq. More than 1.11 billion clean reads were obtained from our available sequenced samples. A total of 160,472 transcripts were generated using Trinity de novo assembly and 4,985 significantly differentially expressed genes were detected in miR156OE plants A11a and A17 using the Medicago truncatula genome as reference. A total of 17 genes (including upregulated, downregulated, and unchanged) were selected for quantitative real-time PCR (qRT-PCR) validation, which showed that gene expression levels were largely consistent between qRT-PCR and RNA-Seq data. In addition to the established SPL genes MsSPL6, MsSPL12 and MsSPL13, four new SPLs; MsSPL2, MsSPL3, MsSPL4 and MsSPL9 were also down-regulated significantly in both miR156OE plants. These seven SPL genes belong to genes phylogeny clades VI, IV, VIII, V and VII, which have been reported to be targeted by miR156 in Arabidopsis thaliana. The gene ontology terms characterized electron transporter, starch synthase activity, sucrose transport, sucrose-phosphate synthase activity, chitin binding, sexual reproduction, flavonoid biosynthesis and lignin catabolism correlate well to the phenotypes of miR156OE alfalfa plants. Conclusions This is the first report of changes in global gene expression in response to miR156 overexpression in alfalfa. The discovered miR156-targeted SPL genes belonging to different clades indicate miR156 plays fundamental and multifunctional roles in regulating alfalfa plant development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3014-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruimin Gao
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Ryan S Austin
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.,Department of Biology, University of Western Ontario, 151 Richmond Street, London, ON, N6A 5B7, Canada
| | - Lisa Amyot
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada. .,Department of Biology, University of Western Ontario, 151 Richmond Street, London, ON, N6A 5B7, Canada.
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