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Wang X, Hu Y, Wang Y, Wang Y, Gao S, Zhang T, Guo J, Shi L. Integrated metabolomic and transcriptomic strategies to reveal alkali-resistance mechanisms in wild soybean during post-germination growth stage. PLANTA 2023; 257:95. [PMID: 37036535 DOI: 10.1007/s00425-023-04129-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
The keys to alkali-stress resistance of barren-tolerant wild soybean lay in enhanced reutilization of reserves in cotyledons as well as improved antioxidant protection and organic acid accumulation in young roots. Soil alkalization of farmlands is increasingly serious, adversely restricting crop growth and endangering food security. Here, based on integrated analysis of transcriptomics and metabolomics, we systematically investigated changes in cotyledon weight and young root growth in response to alkali stress in two ecotypes of wild soybean after germination to reveal alkali-resistance mechanisms in barren-tolerant wild soybean. Compared with barren-tolerant wild soybean, the dry weight of common wild soybean cotyledons under alkali stress decreased slowly and the length of young roots shortened. In barren-tolerant wild soybean, nitrogen-transport amino acids asparagine and glutamate decreased in cotyledons but increased in young roots, and nitrogen-compound transporter genes and genes involved in asparagine metabolism were significantly up-regulated in both cotyledons and young roots. Moreover, isocitric, succinic, and L-malic acids involved in the glyoxylate cycle significantly accumulated and the malate synthetase gene was up-regulated in barren-tolerant wild soybean cotyledons. In barren-tolerant wild soybean young roots, glutamate and glycine related to glutathione metabolism increased significantly and the glutathione reductase gene was up-regulated. Pyruvic acid and citric acid involved in pyruvate-citrate metabolism increased distinctly and genes encoding pyruvate decarboxylase and citrate synthetase were up-regulated. Integrated analysis showed that the keys to alkali-stress resistance of barren-tolerant wild soybean lay in enhanced protein decomposition, amino acid transport, and lipolysis in cotyledons as well as improved antioxidant protection and organic acid accumulation in young roots. This study provides new ideas for the exploitation and utilization of wild soybean resources.
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Affiliation(s)
- Xiaoning Wang
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Yunan Hu
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Yuming Wang
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Yida Wang
- College of Physical Education, Northeast Normal University, Changchun, 130024, China
| | - Shujuan Gao
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Tao Zhang
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Jixun Guo
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Lianxuan Shi
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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Thingnam SS, Lourembam DS, Tongbram PS, Lokya V, Tiwari S, Khan MK, Pandey A, Hamurcu M, Thangjam R. A Perspective Review on Understanding Drought Stress Tolerance in Wild Banana Genetic Resources of Northeast India. Genes (Basel) 2023; 14:genes14020370. [PMID: 36833297 PMCID: PMC9957078 DOI: 10.3390/genes14020370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
The enormous perennial monocotyledonous herb banana (Musa spp.), which includes dessert and cooking varieties, is found in more than 120 countries and is a member of the order Zingiberales and family Musaceae. The production of bananas requires a certain amount of precipitation throughout the year, and its scarcity reduces productivity in rain-fed banana-growing areas due to drought stress. To increase the tolerance of banana crops to drought stress, it is necessary to explore crop wild relatives (CWRs) of banana. Although molecular genetic pathways involved in drought stress tolerance of cultivated banana have been uncovered and understood with the introduction of high-throughput DNA sequencing technology, next-generation sequencing (NGS) techniques, and numerous "omics" tools, unfortunately, such approaches have not been thoroughly implemented to utilize the huge potential of wild genetic resources of banana. In India, the northeastern region has been reported to have the highest diversity and distribution of Musaceae, with more than 30 taxa, 19 of which are unique to the area, accounting for around 81% of all wild species. As a result, the area is regarded as one of the main locations of origin for the Musaceae family. The understanding of the response of the banana genotypes of northeastern India belonging to different genome groups to water deficit stress at the molecular level will be useful for developing and improving drought tolerance in commercial banana cultivars not only in India but also worldwide. Hence, in the present review, we discuss the studies conducted to observe the effect of drought stress on different banana species. Moreover, the article highlights the tools and techniques that have been used or that can be used for exploring and understanding the molecular basis of differentially regulated genes and their networks in different drought stress-tolerant banana genotypes of northeast India, especially wild types, for unraveling their potential novel traits and genes.
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Affiliation(s)
| | | | - Punshi Singh Tongbram
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
| | - Vadthya Lokya
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Robert Thangjam
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
- Department of Life Sciences, School of Life Sciences, Manipur University, Imphal 795003, India
- Correspondence:
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Zhao C, Gangurde SS, Xin X, Varshney RK. Editorial: Creation and utilization of crop germplasm resources. FRONTIERS IN PLANT SCIENCE 2023; 14:1140037. [PMID: 36760642 PMCID: PMC9905828 DOI: 10.3389/fpls.2023.1140037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Sunil S. Gangurde
- Crop Protection and Management Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Tifton, GA, United States
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Xia Xin
- National Crop GeneBank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rajeev K. Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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Gayacharan, Parida SK, Mondal N, Yadav R, Vishwakarma H, Rana JC. Mining legume germplasm for genetic gains: An Indian perspective. Front Genet 2023; 14:996828. [PMID: 36816034 PMCID: PMC9933516 DOI: 10.3389/fgene.2023.996828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023] Open
Abstract
Legumes play a significant role in food and nutritional security and contribute to environmental sustainability. Although legumes are highly beneficial crops, it has not yet been possible to enhance their yield and production to a satisfactory level. Amid a rising population and low yield levels, per capita average legume consumption in India has fallen by 71% over the last 50 years, and this has led to protein-related malnutrition in a large segment of the Indian population, especially women and children. Several factors have hindered attempts to achieve yield enhancement in grain legumes, including biotic and abiotic pressures, a lack of good ideotypes, less amenability to mechanization, poorer responsiveness to fertilizer input, and a poor genetic base. Therefore, there is a need to mine the approximately 0.4 million ex situ collections of legumes that are being conserved in gene banks globally for identification of ideal donors for various traits. The Indian National Gene Bank conserves over 63,000 accessions of legumes belonging to 61 species. Recent initiatives have been undertaken in consortia mode with the aim of unlocking the genetic potential of ex situ collections and conducting large-scale germplasm characterization and evaluation analyses. We assume that large-scale phenotyping integrated with omics-based science will aid the identification of target traits and their use to enhance genetic gains. Additionally, in cases where the genetic base of major legumes is narrow, wild relatives have been evaluated, and these are being exploited through pre-breeding. Thus far, >200 accessions of various legumes have been registered as unique donors for various traits of interest.
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Affiliation(s)
- Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Swarup K. Parida
- DBT-National Institute of Plant Genome Research, New Delhi, India
| | - Nupur Mondal
- Shivaji College, University of Delhi, New Delhi, India
| | - Rashmi Yadav
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Jai C. Rana
- Alliance of Bioversity International and CIAT, India Office, National Agricultural Science Complex, New Delhi, India
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Samuels ME, Lapointe C, Halwas S, Worley AC. Genomic Sequence of Canadian Chenopodium berlandieri: A North American Wild Relative of Quinoa. PLANTS (BASEL, SWITZERLAND) 2023; 12:467. [PMID: 36771551 PMCID: PMC9920564 DOI: 10.3390/plants12030467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Chenopodium berlandieri (pitseed goosefoot) is a widespread native North American plant, which was cultivated and consumed by indigenous peoples prior to the arrival of European colonists. Chenopodium berlandieri is closely related to, and freely hybridizes with the domesticated South American food crop C. quinoa. As such it is a potential source of wild germplasm for breeding with C. quinoa, for improved quinoa production in North America. The C. berlandieri genome sequence could also be a useful source of information for improving quinoa adaptation. To this end, we first optimized barcode markers in two chloroplast genes, rbcL and matK. Together these markers can distinguish C. berlandieri from the morphologically similar Eurasian invasive C. album (lamb's quarters). Second, we performed whole genome sequencing and preliminary assembly of a C. berlandieri accession collected in Manitoba, Canada. Our assembly, while fragmented, is consistent with the expected allotetraploid structure containing diploid Chenopodium sub-genomes A and B. The genome of our accession is highly homozygous, with only one variant site per 3-4000 bases in non-repetitive sequences. This is consistent with predominant self-fertilization. As previously reported for the genome of a partly domesticated Mexican accession of C. berlandieri, our genome assembly is similar to that of C. quinoa. Somewhat unexpectedly, the genome of our accession had almost as many variant sites when compared to the Mexican C. berlandieri, as compared to C. quinoa. Despite the overall similarity of our genome sequence to that of C. quinoa, there are differences in genes known to be involved in the domestication or genetics of other food crops. In one example, our genome assembly appears to lack one functional copy of the SOS1 (salt overly sensitive 1) gene. SOS1 is involved in soil salinity tolerance, and by extension may be relevant to the adaptation of C. berlandieri to the wet climate of the Canadian region where it was collected. Our genome assembly will be a useful tool for the improved cultivation of quinoa in North America.
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Affiliation(s)
- Mark E. Samuels
- Centre de Recherche du CHU Ste-Justine, Montréal, QC H3T 1C5, Canada
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1C5, Canada
- Département de Médecine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Cassandra Lapointe
- Centre de Recherche du CHU Ste-Justine, Montréal, QC H3T 1C5, Canada
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Sara Halwas
- Department of Anthropology, University of Manitoba, Winnipeg, MB R3T 2M8, Canada
| | - Anne C. Worley
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2M8, Canada
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Park MJ, Kim E, Jeong YS, Son MY, Jang Y, Ka KH. Determination and Analysis of Hyper-Variable A Mating Types in Wild Strains of Lentinula edodes in Korea. MYCOBIOLOGY 2023; 51:26-35. [PMID: 36846627 PMCID: PMC9946336 DOI: 10.1080/12298093.2022.2161157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
The diversity of A mating type in wild strains of Lentinula edodes was extensively analyzed to characterize and utilize them for developing new cultivars. One hundred twenty-three A mating type alleles, including 67 newly discovered alleles, were identified from 106 wild strains collected for the past four decades in Korea. Based on previous studies and current findings, a total of 130 A mating type alleles have been found, 124 of which were discovered from wild strains, indicating the hyper-variability of A mating type alleles of L. edodes. About half of the A mating type alleles in wild strains were found in more than two strains, whereas the other half of the alleles were found in only one strain. About 90% of A mating type combinations in dikaryotic wild strains showed a single occurrence. Geographically, diverse A mating type alleles were intensively located in the central region of the Korean peninsula, whereas only allele A17 was observed throughout Korea. We also found the conservation of the TCCCAC motif in addition to the previously reported motifs, including ATTGT, ACAAT, and GCGGAG, in the intergenic regions of A mating loci. Sequence comparison among some alleles indicated that accumulated mutation and recombination would contribute to the diversification of A mating type alleles in L. edodes. Our data support the rapid evolution of A mating locus in L. edodes, and would help to understand the characteristics of A mating loci of wild strains in Korea and help to utilize them for developing new cultivars.
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Affiliation(s)
- Mi-Jeong Park
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
| | - Eunjin Kim
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
| | - Yeun Sug Jeong
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
| | - Mi-Young Son
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
| | - Yeongseon Jang
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
| | - Kang-Hyeon Ka
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Korea
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Chen Y, Ji J, Kong D, Tang X, Wen M, Wang G, Dai K, Shi P, Zhang X, Zhang H, Jiao C, Wang Z, Sun L, Yuan C, Wang H, Zhang X, Sun B, Fei X, Guo H, Xiao J, Wang X. Resistance of QYm.nau-2D to wheat yellow mosaic virus was derived from an alien introgression into common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:3. [PMID: 36651948 DOI: 10.1007/s00122-023-04286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
The QYm.nau-2D locus conferring wheat yellow mosaic virus resistance is an exotic introgression and we developed 11 diagnostic markers tightly linked to QYm.nau-2D. Wheat yellow mosaic virus (WYMV) is a serious disease of winter wheat in China. Breeding resistant varieties is the most effective strategy for WYMV control. A WYMV resistant locus QYm.nau-2D on the chromosome arm 2DL has been repeatedly reported but the mapped region is large. In the present study, we screened recombinants using a biparental population and mapped QYm.nau-2D into an 18.8 Mb physical interval. By genome-wide association studies of 372 wheat varieties for WYMV resistance in four environments, we narrowed down QYm.nau-2D into a 16.4 Mb interval. Haplotype analysis indicated QYm.nau-2D were present as six different states due to recombination during hybridization breeding. QYm.nau-2D was finally mapped into a linkage block of 11.2 Mb. Chromosome painting using 2D specific probes and collinearity analysis among the published sequences corresponding to QYm.nau-2D region indicated the block was an exotic introgression. The Illumina-sequenced reads of four diploid Aegilops species were mapped to the sequence of Fielder, a variety having the introgression. The mapping reads were significantly increased at the putative introgression regions of Fielder. Ae. uniaristata (NN) had the highest mapping reads, suggesting that QYm.nau-2D was possibly an introgression from genome N. We investigated the agronomic performances of different haplotypes and observed no linkage drag of the alien introgression for the 15 tested traits. For marker-assisted selection of QYm.nau-2D, we developed 11 diagnostic markers tightly linked to the locus. This research provided a case study of an exotic introgression, which has been utilized in wheat improvement for WYMV resistance.
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Affiliation(s)
- Yiming Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Jialun Ji
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Dehui Kong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Xiong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Mingxing Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
- Zhenjiang Institute of Agricultural Science, Jurong, Jiangsu, 212400, China
| | - Guoqing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Keli Dai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Peiyao Shi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Xu Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Huajian Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Chengzhi Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Zongkuan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Li Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Chunxia Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Bingjian Sun
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Xinru Fei
- Yandu District Agricultural Science Research Institute, Yancheng, Jiangsu, 224011, China
| | - Hong Guo
- Yandu District Agricultural Science Research Institute, Yancheng, Jiangsu, 224011, China
| | - Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, 210095, China.
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Daldoul S, Hanzouli F, Hamdi Z, Chenenaoui S, Wetzel T, Nick P, Mliki A, Gargouri M. The root transcriptome dynamics reveals new valuable insights in the salt-resilience mechanism of wild grapevine ( Vitis vinifera subsp . sylvestris). FRONTIERS IN PLANT SCIENCE 2022; 13:1077710. [PMID: 36570937 PMCID: PMC9780605 DOI: 10.3389/fpls.2022.1077710] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/16/2022] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Most of elite cultivated grapevine varieties (Vitis vinifera L.), conventionally grafted on rootstocks, are becoming more and more affected by climate changes, such as increase of salinity. Therefore, we revisited the valuable genetic resources of wild grapevines (V. sylvestris) to elaborate strategies for a sustainable viticulture. METHODS Here, we compared physiological and biochemical responses of two salt-tolerant species: a wild grapevine genotype "Tebaba" from our previous studies and the conventional rootstock "1103 Paulsen". Interestingly, our physio-biochemical results showed that under 150mM NaCl, "Tebaba" maintains higher leaf osmotic potential, lower Na+/K+ ratio and a significant peaked increase of polyphenol content at the first 8h of salinity stress. This behavior allowed to hypothesis a drastic repatterning of metabolism in "Tebaba's" roots following a biphasic response. In order to deepen our understanding on the "Tebaba" salt tolerance mechanism, we investigated a time-dependent transcriptomic analysis covering three sampling times, 8h, 24h and 48h. RESULTS The dynamic analysis indicated that "Tebaba" root cells detect and respond on a large scale within 8h to an accumulation of ROS by enhancing a translational reprogramming process and inducing the transcripts of glycolytic metabolism and flavonoids biosynthesis as a predominate non-enzymatic scavenging process. Afterwards, there is a transition to a largely gluconeogenic stage followed by a combined response mechanism based on cell wall remodeling and lignin biosynthesis with an efficient osmoregulation between 24 and 48 h. DISCUSSION This investigation explored for the first time in depth the established cross-talk between the physiological, biochemical and transcriptional regulators contributing to propose a hypothetical model of the dynamic salt mechanism tolerance of wild grapevines. In summary, these findings allowed further understanding of the genetic regulation mechanism of salt-tolerance in V. sylvestris and identified specific candidate genes valuable for appropriate breeding strategies.
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Affiliation(s)
- Samia Daldoul
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Faouzia Hanzouli
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Zohra Hamdi
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Synda Chenenaoui
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Peter Nick
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
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Kashyap A, Garg P, Tanwar K, Sharma J, Gupta NC, Ha PTT, Bhattacharya RC, Mason AS, Rao M. Strategies for utilization of crop wild relatives in plant breeding programs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4151-4167. [PMID: 36136128 DOI: 10.1007/s00122-022-04220-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Crop wild relatives (CWRs) are weedy and wild relatives of the domesticated and cultivated crops, which usually occur and are maintained in natural forms in their centres of origin. These include the ancestors or progenitors of all cultivated species and comprise rich sources of diversity for many important traits useful in plant breeding. CWRs can play an important role in broadening genetic bases and introgression of economical traits into crops, but their direct use by breeders for varietal improvement program is usually not advantageous due to the presence of crossing or chromosome introgression barriers with cultivated species as well as their high frequencies of agronomically undesirable alleles. Linkage drag may subsequently result in unfavourable traits in the subsequent progeny when segments of the genome linked with quantitative trait loci (QTL), or a phenotype, are introgressed from wild germplasm. Here, we first present an overview in regards to the contribution that wild species have made to improve biotic, abiotic stress tolerances and yield-related traits in crop varieties, and secondly summarise the various challenges which are experienced in interspecific hybridization along with their probable solutions. We subsequently suggest techniques for readily harnessing these wild relatives for fast and effective introgression of exotic alleles in pre-breeding research programs.
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Affiliation(s)
- Anamika Kashyap
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Pooja Garg
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Kunal Tanwar
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Jyoti Sharma
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Navin C Gupta
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | - Pham Thi Thu Ha
- Genomic Research Institute & Seed, Ton Duc Thang University, Ho Chi Minh, Vietnam
| | - R C Bhattacharya
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India
| | | | - Mahesh Rao
- ICAR-National Institute for Plant Biotechnology, Pusa, Delhi, India.
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Pisias MT, Bakala HS, McAlvay AC, Mabry ME, Birchler JA, Yang B, Pires JC. Prospects of Feral Crop De Novo Redomestication. PLANT & CELL PHYSIOLOGY 2022; 63:1641-1653. [PMID: 35639623 DOI: 10.1093/pcp/pcac072] [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: 02/14/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Modern agriculture depends on a narrow variety of crop species, leaving global food and nutritional security highly vulnerable to the adverse effects of climate change and population expansion. Crop improvement using conventional and molecular breeding approaches leveraging plant genetic diversity using crop wild relatives (CWRs) has been one approach to address these issues. However, the rapid pace of the global change requires additional innovative solutions to adapt agriculture to meet global needs. Neodomestication-the rapid and targeted introduction of domestication traits using introgression or genome editing of CWRs-is being explored as a supplementary approach. These methods show promise; however, they have so far been limited in efficiency and applicability. We propose expanding the scope of neodomestication beyond truly wild CWRs to include feral crops as a source of genetic diversity for novel crop development, in this case 'redomestication'. Feral crops are plants that have escaped cultivation and evolved independently, typically adapting to their local environments. Thus, feral crops potentially contain valuable adaptive features while retaining some domestication traits. Due to their genetic proximity to crop species, feral crops may be easier targets for de novo domestication (i.e. neodomestication via genome editing techniques). In this review, we explore the potential of de novo redomestication as an application for novel crop development by genome editing of feral crops. This approach to efficiently exploit plant genetic diversity would access an underutilized reservoir of genetic diversity that could prove important in support of global food insecurity in the face of the climate change.
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Affiliation(s)
- Michael T Pisias
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Harmeet Singh Bakala
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
- Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, MO 63132, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
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Bohra A, Tiwari A, Kaur P, Ganie SA, Raza A, Roorkiwal M, Mir RR, Fernie AR, Smýkal P, Varshney RK. The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies. PLANT & CELL PHYSIOLOGY 2022; 63:1554-1572. [PMID: 35713290 PMCID: PMC9680861 DOI: 10.1093/pcp/pcac086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 05/11/2023]
Abstract
Crop domestication is a co-evolutionary process that has rendered plants and animals significantly dependent on human interventions for survival and propagation. Grain legumes have played an important role in the development of Neolithic agriculture some 12,000 years ago. Despite being early companions of cereals in the origin and evolution of agriculture, the understanding of grain legume domestication has lagged behind that of cereals. Adapting plants for human use has resulted in distinct morpho-physiological changes between the wild ancestors and domesticates, and this distinction has been the focus of several studies aimed at understanding the domestication process and the genetic diversity bottlenecks created. Growing evidence from research on archeological remains, combined with genetic analysis and the geographical distribution of wild forms, has improved the resolution of the process of domestication, diversification and crop improvement. In this review, we summarize the significance of legume wild relatives as reservoirs of novel genetic variation for crop breeding programs. We describe key legume features, which evolved in response to anthropogenic activities. Here, we highlight how whole genome sequencing and incorporation of omics-level data have expanded our capacity to monitor the genetic changes accompanying these processes. Finally, we present our perspective on alternative routes centered on de novo domestication and re-domestication to impart significant agronomic advances of novel crops over existing commodities. A finely resolved domestication history of grain legumes will uncover future breeding targets to develop modern cultivars enriched with alleles that improve yield, quality and stress tolerance.
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Affiliation(s)
- Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Abha Tiwari
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kalyanpur, Kanpur 208024, India
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, Santiniketan Road, Bolpur 731235, India
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Sheik Khalifa Bin Zayed Street, Al Ain, Abu Dhabi 15551, UAE
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST, Shalimar, Srinagar 190025, India
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Křížkovského 511/8, Olomouc 78371, Czech Republic
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Tirnaz S, Zandberg J, Thomas WJW, Marsh J, Edwards D, Batley J. Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies. FRONTIERS IN PLANT SCIENCE 2022; 13:1008904. [PMID: 36466237 PMCID: PMC9712971 DOI: 10.3389/fpls.2022.1008904] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/25/2022] [Indexed: 06/01/2023]
Abstract
Global agricultural industries are under pressure to meet the future food demand; however, the existing crop genetic diversity might not be sufficient to meet this expectation. Advances in genome sequencing technologies and availability of reference genomes for over 300 plant species reveals the hidden genetic diversity in crop wild relatives (CWRs), which could have significant impacts in crop improvement. There are many ex-situ and in-situ resources around the world holding rare and valuable wild species, of which many carry agronomically important traits and it is crucial for users to be aware of their availability. Here we aim to explore the available ex-/in- situ resources such as genebanks, botanical gardens, national parks, conservation hotspots and inventories holding CWR accessions. In addition we highlight the advances in availability and use of CWR genomic resources, such as their contribution in pangenome construction and introducing novel genes into crops. We also discuss the potential and challenges of modern breeding experimental approaches (e.g. de novo domestication, genome editing and speed breeding) used in CWRs and the use of computational (e.g. machine learning) approaches that could speed up utilization of CWR species in breeding programs towards crop adaptability and yield improvement.
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Wani SH, Choudhary M, Barmukh R, Bagaria PK, Samantara K, Razzaq A, Jaba J, Ba MN, Varshney RK. Molecular mechanisms, genetic mapping, and genome editing for insect pest resistance in field crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3875-3895. [PMID: 35267056 PMCID: PMC9729161 DOI: 10.1007/s00122-022-04060-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 02/11/2022] [Indexed: 05/03/2023]
Abstract
Improving crop resistance against insect pests is crucial for ensuring future food security. Integrating genomics with modern breeding methods holds enormous potential in dissecting the genetic architecture of this complex trait and accelerating crop improvement. Insect resistance in crops has been a major research objective in several crop improvement programs. However, the use of conventional breeding methods to develop high-yielding cultivars with sustainable and durable insect pest resistance has been largely unsuccessful. The use of molecular markers for identification and deployment of insect resistance quantitative trait loci (QTLs) can fastrack traditional breeding methods. Till date, several QTLs for insect pest resistance have been identified in field-grown crops, and a few of them have been cloned by positional cloning approaches. Genome editing technologies, such as CRISPR/Cas9, are paving the way to tailor insect pest resistance loci for designing crops for the future. Here, we provide an overview of diverse defense mechanisms exerted by plants in response to insect pest attack, and review recent advances in genomics research and genetic improvements for insect pest resistance in major field crops. Finally, we discuss the scope for genomic breeding strategies to develop more durable insect pest resistant crops.
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Affiliation(s)
- Shabir H Wani
- Mountain Research Center for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, J&K, 192101, India.
| | - Mukesh Choudhary
- ICAR-Indian Institute of Maize Research (ICAR-IIMR), PAU Campus, Ludhiana, Punjab, 141001, India
| | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Pravin K Bagaria
- ICAR-Indian Institute of Maize Research (ICAR-IIMR), PAU Campus, Ludhiana, Punjab, 141001, India
| | - Kajal Samantara
- Department of Genetics and Plant Breeding, Centurion University of Technology and Management, Paralakhemundi, Odisha, 761211, India
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Jagdish Jaba
- Intergated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Malick Niango Ba
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), BP 12404, Niamey, Niger
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
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Naqvi RZ, Siddiqui HA, Mahmood MA, Najeebullah S, Ehsan A, Azhar M, Farooq M, Amin I, Asad S, Mukhtar Z, Mansoor S, Asif M. Smart breeding approaches in post-genomics era for developing climate-resilient food crops. FRONTIERS IN PLANT SCIENCE 2022; 13:972164. [PMID: 36186056 PMCID: PMC9523482 DOI: 10.3389/fpls.2022.972164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Improving the crop traits is highly required for the development of superior crop varieties to deal with climate change and the associated abiotic and biotic stress challenges. Climate change-driven global warming can trigger higher insect pest pressures and plant diseases thus affecting crop production sternly. The traits controlling genes for stress or disease tolerance are economically imperative in crop plants. In this scenario, the extensive exploration of available wild, resistant or susceptible germplasms and unraveling the genetic diversity remains vital for breeding programs. The dawn of next-generation sequencing technologies and omics approaches has accelerated plant breeding by providing the genome sequences and transcriptomes of several plants. The availability of decoded plant genomes offers an opportunity at a glance to identify candidate genes, quantitative trait loci (QTLs), molecular markers, and genome-wide association studies that can potentially aid in high throughput marker-assisted breeding. In recent years genomics is coupled with marker-assisted breeding to unravel the mechanisms to harness better better crop yield and quality. In this review, we discuss the aspects of marker-assisted breeding and recent perspectives of breeding approaches in the era of genomics, bioinformatics, high-tech phonemics, genome editing, and new plant breeding technologies for crop improvement. In nutshell, the smart breeding toolkit in the post-genomics era can steadily help in developing climate-smart future food crops.
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Singh M, Kumar S, Mehra R, Sood S, Malhotra N, Sinha R, Jamwal S, Gupta V. Evaluation and identification of advanced lentil interspecific derivatives resulted in the development of early maturing, high yielding, and disease-resistant cultivars under Indian agro-ecological conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:936572. [PMID: 36161028 PMCID: PMC9499259 DOI: 10.3389/fpls.2022.936572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
The genetic base revealed by pedigree records of the majority of released cultivars appears to be narrow in major pulse crops, including lentils, because of the frequent use of the same parents and their derivatives in crop improvement programs. Therefore, corrective measures are needed to widen the genetic base by involving the genetic resources of a distinct gene pool. In this direction, rigorous efforts were made to introgress wild Lens taxa, L. culinaris ssp. orientalis, and L. ervoides into the backgrounds of cultivated varieties. Subsequently, genetic materials were advanced through the single seed descent method of breeding along with a rapid generation advancement (normal and off-season) approach. Two F10:11 interspecific derivatives of lentils were evaluated in augmented block design at two locations, viz. International Centre for Agricultural Research in Dry Areas (ICARDA) and Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), India. The analysis of variance showed remarkable variability for all target characters at both locations. The heritability estimates were high, and correlation analysis exhibited a significant association between the majority of traits assessed at ICARDA and SKUAST, India. Further, SKUAST identified the most promising lines as "Jammu Lentil 144" and "Jammu Lentil 71." These derivatives were further validated separately for their agronomic potential and resistance against major biotic stresses. The results revealed that Jammu Lentil 144 and Jammu Lentil 71 produced 16.65 and 9.40% more seed yield than local and national checks, including earliness, by 25 and 15 days, respectively. These promising interspecific derivatives were also found to be resistant to fusarium wilt, root rot, pod borer, and aphid infestations. The standard agronomy of these cultivars has also been assessed consecutively for 2 years at SKUAST. Overall, the pre-breeding efforts have resulted in the development of early maturing, high-yielding, and disease-resistant lentil cultivars for the Jammu region of India.
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Affiliation(s)
- Mohar Singh
- ICAR-National Bureau of Plant Genetic Resources, Shimla, India
| | - Sanjeev Kumar
- Department of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Reena Mehra
- International Center for Agricultural Research in Dry Areas-Food Legume Research Platform, Bhopal, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla, India
| | - Nikhil Malhotra
- ICAR-National Bureau of Plant Genetic Resources, Shimla, India
| | - Reena Sinha
- Advanced Centre for Rainfed Agriculture Dhiansar, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Sonika Jamwal
- Advanced Centre for Rainfed Agriculture Dhiansar, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Vikas Gupta
- Advanced Centre for Rainfed Agriculture Dhiansar, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
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Kalve S, Gali KK, Tar’an B. Genome-wide association analysis of stress tolerance indices in an interspecific population of chickpea. FRONTIERS IN PLANT SCIENCE 2022; 13:933277. [PMID: 36061786 PMCID: PMC9437449 DOI: 10.3389/fpls.2022.933277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Chickpea is a cool season crop that is highly vulnerable to abiotic stresses such as heat and drought. High temperature during early flowering and pod development stages significantly reduces the crop yield. The wild relatives of chickpeas can be potential donors for the introgression of heat and drought tolerance into cultivated chickpeas for crop improvement. Initially, 600 interspecific lines were derived from crosses between two elite cultivars, CDC Leader (kabuli chickpea) and CDC Consul (desi chickpea), and 20 accessions of Cicer reticulatum. The F5 interspecific lines were tested for agronomic and seed quality traits including reaction to ascochyta blight disease under field conditions at two locations in 2018. A subset of 195 lines were selected based on resistance to ascochyta blight and acceptable seed quality. These lines were evaluated for their performance under suboptimal conditions at Lucky Lake (2019 and 2020) and Moose Jaw (2019), Saskatchewan, Canada, and Yuma, Arizona, United States (2019-2020). The lines were grown and evaluated at two seeding dates, normal (SD1) and late (SD2) seeding dates, at each location and year. The same lines were genotyped using Cicer60K Axiom® SNP chip. The population structure was determined based on 35,431 informative SNPs using fastStructure, and the interspecific lines were clustered at a k-value of 15. Significant marker-trait associations were identified for seed yield from SD1 and SD2 seeding dates, and stress tolerance indices (ATI, K1STI, MP, SSPI, and TOL) using phenotypic values both from individual locations and combined analyses based on BLUP values. SNP marker Ca2_34600347 was significantly associated with yield from both the seeding dates. This and other SNP markers identified in this study may be useful for marker-assisted introgression of abiotic stress tolerance in chickpea.
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Sandhu KS, Shiv A, Kaur G, Meena MR, Raja AK, Vengavasi K, Mall AK, Kumar S, Singh PK, Singh J, Hemaprabha G, Pathak AD, Krishnappa G, Kumar S. Integrated Approach in Genomic Selection to Accelerate Genetic Gain in Sugarcane. PLANTS 2022; 11:plants11162139. [PMID: 36015442 PMCID: PMC9412483 DOI: 10.3390/plants11162139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022]
Abstract
Marker-assisted selection (MAS) has been widely used in the last few decades in plant breeding programs for the mapping and introgression of genes for economically important traits, which has enabled the development of a number of superior cultivars in different crops. In sugarcane, which is the most important source for sugar and bioethanol, marker development work was initiated long ago; however, marker-assisted breeding in sugarcane has been lagging, mainly due to its large complex genome, high levels of polyploidy and heterozygosity, varied number of chromosomes, and use of low/medium-density markers. Genomic selection (GS) is a proven technology in animal breeding and has recently been incorporated in plant breeding programs. GS is a potential tool for the rapid selection of superior genotypes and accelerating breeding cycle. However, its full potential could be realized by an integrated approach combining high-throughput phenotyping, genotyping, machine learning, and speed breeding with genomic selection. For better understanding of GS integration, we comprehensively discuss the concept of genetic gain through the breeder’s equation, GS methodology, prediction models, current status of GS in sugarcane, challenges of prediction accuracy, challenges of GS in sugarcane, integrated GS, high-throughput phenotyping (HTP), high-throughput genotyping (HTG), machine learning, and speed breeding followed by its prospective applications in sugarcane improvement.
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Affiliation(s)
- Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Aalok Shiv
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Mintu Ram Meena
- Regional Center, ICAR-Sugarcane Breeding Institute, Karnal 132001, India
| | - Arun Kumar Raja
- Division of Crop Production, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Krishnapriya Vengavasi
- Division of Crop Production, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Ashutosh Kumar Mall
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Sanjeev Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Praveen Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Jyotsnendra Singh
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Govind Hemaprabha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Ashwini Dutt Pathak
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Gopalareddy Krishnappa
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
- Correspondence: (G.K.); (S.K.)
| | - Sanjeev Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
- Correspondence: (G.K.); (S.K.)
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Harnessing adult-plant resistance genes to deploy durable disease resistance in crops. Essays Biochem 2022; 66:571-580. [PMID: 35912968 PMCID: PMC9528086 DOI: 10.1042/ebc20210096] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022]
Abstract
Adult-plant resistance (APR) is a type of genetic resistance in cereals that is effective during the later growth stages and can protect plants from a range of disease-causing pathogens. Our understanding of the functions of APR-associated genes stems from the well-studied wheat-rust pathosystem. Genes conferring APR can offer pathogen-specific resistance or multi-pathogen resistance, whereby resistance is activated following a molecular recognition event. The breeding community prefers APR to other types of resistance because it offers broad-spectrum protection that has proven to be more durable. In practice, however, deployment of new cultivars incorporating APR is challenging because there is a lack of well-characterised APRs in elite germplasm and multiple loci must be combined to achieve high levels of resistance. Genebanks provide an excellent source of genetic diversity that can be used to diversify resistance factors, but introgression of novel alleles into elite germplasm is a lengthy and challenging process. To overcome this bottleneck, new tools in breeding for resistance must be integrated to fast-track the discovery, introgression and pyramiding of APR genes. This review highlights recent advances in understanding the functions of APR genes in the well-studied wheat-rust pathosystem, the opportunities to adopt APR genes in other crops and the technology that can speed up the utilisation of new sources of APR in genebank accessions.
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Qiu QS, Melino VJ, Zhao Z, Qi Z, Sweetman C, Roessner U. Editorial: Salinity tolerance: From model or wild plants to adapted crops. FRONTIERS IN PLANT SCIENCE 2022; 13:985057. [PMID: 35968101 PMCID: PMC9364423 DOI: 10.3389/fpls.2022.985057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Quan-Sheng Qiu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining, China
| | - Vanessa Jane Melino
- Center for Desert Agriculture and Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Zhiguang Zhao
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining, China
| | - Zhi Qi
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, China
| | - Crystal Sweetman
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Ute Roessner
- Research School of Biology, The Australian National University, Acton, ACT, Australia
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Eastwood RJ, Tambam BB, Aboagye LM, Akparov ZI, Aladele SE, Allen R, Amri A, Anglin NL, Araya R, Arrieta-Espinoza G, Asgerov A, Awang K, Awas T, Barata AM, Boateng SK, Magos Brehm J, Breidy J, Breman E, Brenes Angulo A, Burle ML, Castañeda-Álvarez NP, Casimiro P, Chaves NF, Clemente AS, Cockel CP, Davey A, De la Rosa L, Debouck DG, Dempewolf H, Dokmak H, Ellis D, Faruk A, Freitas C, Galstyan S, García RM, Ghimire KH, Guarino L, Harker R, Hope R, Humphries AW, Jamora N, Jatoi SA, Khutsishvili M, Kikodze D, Kyratzis AC, León-Lobos P, Liu U, Mainali RP, Mammadov AT, Manrique-Carpintero NC, Manzella D, Mat Ali MS, Medeiros MB, Guzmán MAM, Mikatadze-Pantsulaia T, Mohamed ETI, Monteros-Altamirano Á, Morales A, Müller JV, Mulumba JW, Nersesyan A, Nóbrega H, Nyamongo DO, Obreza M, Okere AU, Orsenigo S, Ortega-Klose F, Papikyan A, Pearce TR, Pinheiro de Carvalho MAA, Prohens J, Rossi G, Salas A, Singh Shrestha D, Siddiqui SU, Smith PP, Sotomayor DA, Tacán M, Tapia C, Toledo Á, Toll J, Vu DT, Vu TD, Way MJ, Yazbek M, Zorrilla C, Kilian B. Adapting Agriculture to Climate Change: A Synopsis of Coordinated National Crop Wild Relative Seed Collecting Programs across Five Continents. PLANTS 2022; 11:plants11141840. [PMID: 35890473 PMCID: PMC9319254 DOI: 10.3390/plants11141840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
The Adapting Agriculture to Climate Change Project set out to improve the diversity, quantity, and accessibility of germplasm collections of crop wild relatives (CWR). Between 2013 and 2018, partners in 25 countries, heirs to the globetrotting legacy of Nikolai Vavilov, undertook seed collecting expeditions targeting CWR of 28 crops of global significance for agriculture. Here, we describe the implementation of the 25 national collecting programs and present the key results. A total of 4587 unique seed samples from at least 355 CWR taxa were collected, conserved ex situ, safety duplicated in national and international genebanks, and made available through the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture (Plant Treaty). Collections of CWR were made for all 28 targeted crops. Potato and eggplant were the most collected genepools, although the greatest number of primary genepool collections were made for rice. Overall, alfalfa, Bambara groundnut, grass pea and wheat were the genepools for which targets were best achieved. Several of the newly collected samples have already been used in pre-breeding programs to adapt crops to future challenges.
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Affiliation(s)
- Ruth J. Eastwood
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
- Correspondence:
| | - Beri B. Tambam
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Lawrence M. Aboagye
- CSIR—Plant Genetic Resources Research Institute, Bunso P.O. Box 7, Ghana; (L.M.A.); (S.K.B.)
| | - Zeynal I. Akparov
- Genetic Resources Institute of Azerbaijan NAS, 155 Azadlig Avenue, Baku AZ1106, Azerbaijan; (Z.I.A.); (A.A.); (A.T.M.)
| | - Sunday E. Aladele
- National Centre for Genetic Resources and Biotechnology, Moor Plantation, Ibadan PMB 5382, Nigeria; (S.E.A.); (A.U.O.)
| | - Richard Allen
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Ahmed Amri
- The International Center for Agricultural Research in the Dry Areas, Dalia Bldg, 2nd Floor Bashir El Kassar Street Verdun, Beirut 1108-2010, Lebanon; (A.A.); (M.Y.)
| | - Noelle L. Anglin
- USDA ARS Small Grains and Potato Germplasm Research, 1691 S 2700 W, Aberdeen, ID 83210, USA;
| | - Rodolfo Araya
- Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa Rica, 3 km W of Catholic Church of Barrio San José, La Garita, Alajuela 183-4050, Costa Rica; (R.A.); (N.F.C.)
| | - Griselda Arrieta-Espinoza
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, Ciudad de la Investigación—C.P., San José 11501-2050, Costa Rica;
| | - Aydin Asgerov
- Genetic Resources Institute of Azerbaijan NAS, 155 Azadlig Avenue, Baku AZ1106, Azerbaijan; (Z.I.A.); (A.A.); (A.T.M.)
| | - Khadijah Awang
- Malaysian Agricultural Research and Development Institute (MARDI), Persiaran MARDI-UPM, Serdang 43400, Malaysia; (K.A.); (M.S.M.A.)
| | - Tesfaye Awas
- Ethiopian Biodiversity Institute, Comoros Street, Yeka Subcity, Addis Ababa P.O. Box 30726, Ethiopia;
| | - Ana Maria Barata
- Banco Português de Germoplasma Vegetal, INIAV, Quinta de S. José, São Pedro de Merelim, 4700-859 Braga, Portugal;
| | - Samuel Kwasi Boateng
- CSIR—Plant Genetic Resources Research Institute, Bunso P.O. Box 7, Ghana; (L.M.A.); (S.K.B.)
| | - Joana Magos Brehm
- Jardim Botânico, Museu Nacional de Historia Natural e da Ciência, Universidade de Lisboa, R. da Escola Politécnica 56, 1250-102 Lisboa, Portugal; (J.M.B.); (A.S.C.)
| | - Joelle Breidy
- Lebanese Agricultural Research Institute, Tal Amara, Rayak P.O. Box 287, Lebanon; (J.B.); (H.D.)
| | - Elinor Breman
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Arturo Brenes Angulo
- Centro de Investigaciones Agronómicas, Universidad de Costa Rica, San José 11501-2060, Costa Rica;
| | - Marília L. Burle
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Av. W5 Norte (Final), Brasília 70770-917, DF, Brazil; (M.L.B.); (M.B.M.)
| | - Nora P. Castañeda-Álvarez
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Pedro Casimiro
- Direção Regional do Ambiente e Alterações Climáticas, Rua Cônsul Dabney, Colónia Alemã, Apartado 140, 9900-014 Horta, Portugal;
| | - Néstor F. Chaves
- Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa Rica, 3 km W of Catholic Church of Barrio San José, La Garita, Alajuela 183-4050, Costa Rica; (R.A.); (N.F.C.)
| | - Adelaide S. Clemente
- Jardim Botânico, Museu Nacional de Historia Natural e da Ciência, Universidade de Lisboa, R. da Escola Politécnica 56, 1250-102 Lisboa, Portugal; (J.M.B.); (A.S.C.)
| | - Christopher P. Cockel
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Alexandra Davey
- Fauna & Flora International, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; (A.D.); (R.H.)
| | - Lucía De la Rosa
- Plant Genetic Resources Centre, National Institute for Agricultural and Food Research and Technology (CRF-INIA), CSIC, Finca La Canaleja, A2 km 36, 28800 Alcalá de Henares, Spain; (L.D.l.R.); (R.M.G.)
| | - Daniel G. Debouck
- Alliance Bioversity International Center of Tropical Agriculture, km 17, Recta Cali-Palmira, Apartado Aéreo 6713, Cali 763537, Colombia;
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Hiba Dokmak
- Lebanese Agricultural Research Institute, Tal Amara, Rayak P.O. Box 287, Lebanon; (J.B.); (H.D.)
| | - David Ellis
- International Potato Center, Avenida La Molina 1895, La Molina, Lima 15023, Peru; (D.E.); (N.C.M.-C.); (A.S.)
| | - Aisyah Faruk
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Cátia Freitas
- Banco de Sementes dos Açores, Rua de São Lourenço, nº 23 Flamengos, 9900-401 Horta, Portugal;
| | - Sona Galstyan
- Institute of Botany after A. Takhtajyan of the National Academy of Sciences of the Republic of Armenia, Acharyan Street 1, Yerevan 0040, Armenia; (S.G.); (A.N.); (A.P.)
| | - Rosa M. García
- Plant Genetic Resources Centre, National Institute for Agricultural and Food Research and Technology (CRF-INIA), CSIC, Finca La Canaleja, A2 km 36, 28800 Alcalá de Henares, Spain; (L.D.l.R.); (R.M.G.)
| | - Krishna H. Ghimire
- National Agriculture Genetic Resources Centre, Nepal Agricultural Research Council (NARC), Khumaltar, Lalitpur P.O. Box. 3605, Nepal; (K.H.G.); (R.P.M.); (D.S.S.)
| | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Ruth Harker
- Natural England, Foss House, Kings Pool, 1-2 Peasholme Green, York YO1 7PX, UK;
| | - Roberta Hope
- Fauna & Flora International, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; (A.D.); (R.H.)
| | - Alan W. Humphries
- South Australian Research and Development Institute, Plant Research Centre, Waite Precinct, Gate 2b Hartley Grove, Urrbrae, SA 5064, Australia;
| | - Nelissa Jamora
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Shakeel Ahmad Jatoi
- Bio-Resources Conservation Institute, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan; (S.A.J.); (S.U.S.)
| | - Manana Khutsishvili
- Institute of Botany, Ilia State University, 1 Botanikuri str., 0105 Tbilisi, Georgia; (M.K.); (D.K.)
| | - David Kikodze
- Institute of Botany, Ilia State University, 1 Botanikuri str., 0105 Tbilisi, Georgia; (M.K.); (D.K.)
| | - Angelos C. Kyratzis
- Agricultural Research Institute, Athalassa, P.O. Box 22016, Nicosia 1516, Cyprus;
| | - Pedro León-Lobos
- Instituto de Investigaciones Agropecuarias, Fidel Oteíza 1956, Pisos 12, Providencia, Santiago 8320000, Chile; (P.L.-L.); (F.O.-K.)
| | - Udayangani Liu
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Ram P. Mainali
- National Agriculture Genetic Resources Centre, Nepal Agricultural Research Council (NARC), Khumaltar, Lalitpur P.O. Box. 3605, Nepal; (K.H.G.); (R.P.M.); (D.S.S.)
| | - Afig T. Mammadov
- Genetic Resources Institute of Azerbaijan NAS, 155 Azadlig Avenue, Baku AZ1106, Azerbaijan; (Z.I.A.); (A.A.); (A.T.M.)
| | | | | | - Mohd Shukri Mat Ali
- Malaysian Agricultural Research and Development Institute (MARDI), Persiaran MARDI-UPM, Serdang 43400, Malaysia; (K.A.); (M.S.M.A.)
| | - Marcelo B. Medeiros
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Av. W5 Norte (Final), Brasília 70770-917, DF, Brazil; (M.L.B.); (M.B.M.)
| | - María A. Mérida Guzmán
- Institute of Agricultural Science and Technology, km 21.5 Highway to the Pacific, Bárcena, Villa Nueva, Guatemala;
| | | | - El Tahir Ibrahim Mohamed
- Agricultural Plant Genetic Resources Conservation and Research Centre, Agricultural Research Corporation, Wad Medani P.O. Box 126, Sudan;
| | - Álvaro Monteros-Altamirano
- Instituto Nacional de Investigaciones Agropecuarias, Avenida Amazonas y Eloy Alfaro, Edificio MAG, Cuarto Piso, Quito 170518, Ecuador; (Á.M.-A.); (M.T.); (C.T.)
| | - Aura Morales
- Centro Nacional de Tecnología “Enrique Álvarez Córdova”, km 33.5 Carretera a Santa Ana, San Andrés, Ciudad Arce, La Libertad, El Salvador;
| | - Jonas V. Müller
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - John W. Mulumba
- Plant Genetic Resources Centre, National Agricultural Research Organization, Plot 2-4 Berkeley Road, Entebbe P.O. Box 40, Uganda;
| | - Anush Nersesyan
- Institute of Botany after A. Takhtajyan of the National Academy of Sciences of the Republic of Armenia, Acharyan Street 1, Yerevan 0040, Armenia; (S.G.); (A.N.); (A.P.)
| | - Humberto Nóbrega
- ISOPlexis—Centro de Agricultura Sustentável e Tecnologia Alimentar, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal; (M.A.A.P.d.C.); (H.N.)
| | - Desterio O. Nyamongo
- Kenya Agricultural and Livestock Research Organisation, Genetic Resources Research Institute, Nairobi P.O. Box 30148-00100, Kenya;
| | - Matija Obreza
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Anthony U. Okere
- National Centre for Genetic Resources and Biotechnology, Moor Plantation, Ibadan PMB 5382, Nigeria; (S.E.A.); (A.U.O.)
| | - Simone Orsenigo
- Department of Earth and Environmental Sciences, Pavia University, Via Sant’Epifanio 14, 27100 Pavia, Italy; (S.O.); (G.R.)
| | - Fernando Ortega-Klose
- Instituto de Investigaciones Agropecuarias, Fidel Oteíza 1956, Pisos 12, Providencia, Santiago 8320000, Chile; (P.L.-L.); (F.O.-K.)
| | - Astghik Papikyan
- Institute of Botany after A. Takhtajyan of the National Academy of Sciences of the Republic of Armenia, Acharyan Street 1, Yerevan 0040, Armenia; (S.G.); (A.N.); (A.P.)
| | - Timothy R. Pearce
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Miguel A. A. Pinheiro de Carvalho
- ISOPlexis—Centro de Agricultura Sustentável e Tecnologia Alimentar, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal; (M.A.A.P.d.C.); (H.N.)
- CITAB—Centro de Investigação e Tecnologias Agroambientais e Biológicas, 5001-801 Vila Real, Portugal
| | - Jaime Prohens
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain;
| | - Graziano Rossi
- Department of Earth and Environmental Sciences, Pavia University, Via Sant’Epifanio 14, 27100 Pavia, Italy; (S.O.); (G.R.)
| | - Alberto Salas
- International Potato Center, Avenida La Molina 1895, La Molina, Lima 15023, Peru; (D.E.); (N.C.M.-C.); (A.S.)
| | - Deepa Singh Shrestha
- National Agriculture Genetic Resources Centre, Nepal Agricultural Research Council (NARC), Khumaltar, Lalitpur P.O. Box. 3605, Nepal; (K.H.G.); (R.P.M.); (D.S.S.)
| | - Sadar Uddin Siddiqui
- Bio-Resources Conservation Institute, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan; (S.A.J.); (S.U.S.)
| | - Paul P. Smith
- Botanic Gardens Conservation International, Descanso House, 199 Kew Road, Richmond TW9 3BW, UK;
| | - Diego A. Sotomayor
- Subdirección de Recursos Genéticos, Instituto Nacional de Innovación Agraria, Av. La Molina 1981, La Molina, Lima 15024, Peru;
- Facultad de Ciencias, Universidad Nacional Agraria La Molina, Av. La Molina s/n, La Molina, Lima 15024, Peru
| | - Marcelo Tacán
- Instituto Nacional de Investigaciones Agropecuarias, Avenida Amazonas y Eloy Alfaro, Edificio MAG, Cuarto Piso, Quito 170518, Ecuador; (Á.M.-A.); (M.T.); (C.T.)
| | - César Tapia
- Instituto Nacional de Investigaciones Agropecuarias, Avenida Amazonas y Eloy Alfaro, Edificio MAG, Cuarto Piso, Quito 170518, Ecuador; (Á.M.-A.); (M.T.); (C.T.)
| | - Álvaro Toledo
- Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla s/n, 00153 Roma, Italy;
| | - Jane Toll
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Dang Toan Vu
- Plant Resources Center, Vietnam Academy of Agricultural Sciences, An Khanh, Hoai Duc, Ha Noi 131000, Vietnam; (D.T.V.); (T.D.V.)
| | - Tuong Dang Vu
- Plant Resources Center, Vietnam Academy of Agricultural Sciences, An Khanh, Hoai Duc, Ha Noi 131000, Vietnam; (D.T.V.); (T.D.V.)
| | - Michael J. Way
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Mariana Yazbek
- The International Center for Agricultural Research in the Dry Areas, Dalia Bldg, 2nd Floor Bashir El Kassar Street Verdun, Beirut 1108-2010, Lebanon; (A.A.); (M.Y.)
| | - Cinthya Zorrilla
- Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Plant Breeding and Genetics Section, 1400 Vienna, Austria;
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
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71
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Roy AK, Chakraborti M, Radhakrishna A, Dwivedi KK, Srivastava MK, Saxena S, Paul S, Khare A, Malaviya DR, Kaushal P. Alien genome mobilization and fixation utilizing an apomixis mediated genome addition (AMGA) strategy in Pennisetum to improve domestication traits of P. squamulatum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2555-2575. [PMID: 35726065 DOI: 10.1007/s00122-022-04138-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
An approach to release 'frozen' variability in apomictic species using sexuality of another species, eventually its utilization in crop improvement and de-novo domestication of crop wild relatives is presented. Pennisetum squamulatum, a secondary gene pool species of pearl millet (P. glaucum), harbours many desirable traits. However, it was neither utilized to improve pearl millet fodder traits nor improvement of its own domestication traits was attempted, due to the complexities of genomes and apomictic reproduction. To overcome this, we followed an Apomixis Mediated Genome Addition (AMGA) strategy and utilized the contrasting reproductive capacities (sexuality and apomixis) of both the species to access the otherwise un-available variability embedded in P. squamulatum. Segregating population of interspecific hybrids exhibited significant variability and heterosis for desired morphological, agronomical, and nutritional traits. Elite apomictic and perennial hybrids were evaluated in breeding trials, and eventually a novel grass cultivar was released for commercial cultivation in India. The performance of newly developed cultivar was superior to other adapted perennial grasses of arid and semi-arid rangelands. Through AMGA, the sexuality of one species was successfully utilized to 'release' the 'frozen' variability embedded in another species. Subsequently, the hybrids representing desirable trait combinations were again 'fixed' utilizing the apomixis alleles from the male parent in a back-and-forth apomixis-sexual-apomixis selection cycle. This study also demonstrated the potential of AMGA to improve crop relatives through genomes introgression as well as de novo domestication of new crops from wild species.
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Affiliation(s)
- A K Roy
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - M Chakraborti
- ICAR - National Rice Research Institute, Cuttack, 753006, India
| | - A Radhakrishna
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - K K Dwivedi
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - M K Srivastava
- ICAR - Indian Institute of Soybean Research, Indore, 452001, India
| | - S Saxena
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - S Paul
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - Aarti Khare
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - D R Malaviya
- ICAR - Indian Institute of Sugarcane Research, Lucknow, 226002, India
| | - P Kaushal
- ICAR - National Institute of Biotic Stress Management, Raipur, 493225, India.
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72
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Zhao Y, Zhu X, Chen X, Zhou JM. From plant immunity to crop disease resistance. J Genet Genomics 2022; 49:693-703. [PMID: 35728759 DOI: 10.1016/j.jgg.2022.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Plant diseases caused by diverse pathogens lead to serious reduction in crop yield and threaten food security worldwide. Genetic improvement of plant immunity is considered as the most effective and sustainable approach to control crop diseases. In the last decade, our understanding of plant immunity at both molecular and genomic levels has improved greatly. Combined with advances in biotechnologies, particularly CRISPR/Cas9-based genome editing, we can now rapidly identify new resistance genes and engineer disease resistance crop plants like never before. In this review, we summarize the current knowledge of plant immunity and outline existing and new strategies for disease resistance improvement in crop plants. We also discuss existing challenges in this field and suggest directions for future studies.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaobo Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China.
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainai 572025, China.
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73
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Renzi JP, Coyne CJ, Berger J, von Wettberg E, Nelson M, Ureta S, Hernández F, Smýkal P, Brus J. How Could the Use of Crop Wild Relatives in Breeding Increase the Adaptation of Crops to Marginal Environments? FRONTIERS IN PLANT SCIENCE 2022; 13:886162. [PMID: 35783966 PMCID: PMC9243378 DOI: 10.3389/fpls.2022.886162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/11/2022] [Indexed: 06/01/2023]
Abstract
Alongside the use of fertilizer and chemical control of weeds, pests, and diseases modern breeding has been very successful in generating cultivars that have increased agricultural production several fold in favorable environments. These typically homogeneous cultivars (either homozygous inbreds or hybrids derived from inbred parents) are bred under optimal field conditions and perform well when there is sufficient water and nutrients. However, such optimal conditions are rare globally; indeed, a large proportion of arable land could be considered marginal for agricultural production. Marginal agricultural land typically has poor fertility and/or shallow soil depth, is subject to soil erosion, and often occurs in semi-arid or saline environments. Moreover, these marginal environments are expected to expand with ongoing climate change and progressive degradation of soil and water resources globally. Crop wild relatives (CWRs), most often used in breeding as sources of biotic resistance, often also possess traits adapting them to marginal environments. Wild progenitors have been selected over the course of their evolutionary history to maintain their fitness under a diverse range of stresses. Conversely, modern breeding for broad adaptation has reduced genetic diversity and increased genetic vulnerability to biotic and abiotic challenges. There is potential to exploit genetic heterogeneity, as opposed to genetic uniformity, in breeding for the utilization of marginal lands. This review discusses the adaptive traits that could improve the performance of cultivars in marginal environments and breeding strategies to deploy them.
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Affiliation(s)
- Juan Pablo Renzi
- Instituto Nacional de Tecnología Agropecuaria, Hilario Ascasubi, Argentina
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | | | - Jens Berger
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia
| | - Eric von Wettberg
- Department of Plant and Soil Science, Gund Institute for Environment, University of Vermont, Burlington, VT, United States
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Matthew Nelson
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Soledad Ureta
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | - Fernando Hernández
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Sciences, Palacký University, Olomouc, Czechia
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Manda L, Idohou R, Assogbadjo AE, Agbangla C. Climate Change Reveals Contractions and Expansions in the Distribution of Suitable Habitats for the Neglected Crop Wild Relatives of the Genus Vigna (Savi) in Benin. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.870041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sustainable conservation of crop wild relatives is one of the pathways to securing global food security amid climate change threats to biodiversity. However, their conservation is partly limited by spatio-temporal distribution knowledge gaps mostly because they are not morphologically charismatic species to attract conservation attention. Therefore, to contribute to the conservation planning of crop wild relatives, this study assessed the present-day distribution and predicted the potential effect of climate change on the distribution of 15 Vigna crop wild relative taxa in Benin under two future climate change scenarios (RCP 4.5 and RCP 8.5) at the 2055-time horizon. MaxEnt model, species occurrence records, and a combination of climate- and soil-related variables were used. The model performed well (AUC, mean = 0.957; TSS, mean = 0.774). The model showed that (i) precipitation of the driest quarter and isothermality were the dominant environmental variables influencing the distribution of the 15 wild Vigna species in Benin; (ii) about half of the total land area of Benin was potentially a suitable habitat of the studied species under the present climate; (iii) nearly one-third of the species may shift their potentially suitable habitat ranges northwards and about half of the species may lose their suitable habitats by 5 to 40% by 2055 due to climate change; and (iv) the existing protected area network in Benin was ineffective in conserving wild Vigna under the current or future climatic conditions, as it covered only about 10% of the total potentially suitable habitat of the studied species. The study concludes that climate change will have both negative and positive effects on the habitat suitability distribution of Vigna crop wild relatives in Benin such that the use of the existing protected areas alone may not be the only best option to conserve the wild Vigna diversity. Integrating multiple in situ and ex situ conservation approaches taking into account “other effective area-based conservation measures” is recommended. This study provides a crucial step towards the development of sustainable conservation strategies for Vigna crop wild relatives in Benin and West Africa.
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Eyland D, Luchaire N, Cabrera‐Bosquet L, Parent B, Janssens SB, Swennen R, Welcker C, Tardieu F, Carpentier SC. High-throughput phenotyping reveals differential transpiration behaviour within the banana wild relatives highlighting diversity in drought tolerance. PLANT, CELL & ENVIRONMENT 2022; 45:1647-1663. [PMID: 35297073 PMCID: PMC9310827 DOI: 10.1111/pce.14310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Crop wild relatives, the closely related species of crops, may harbour potentially important sources of new allelic diversity for (a)biotic tolerance or resistance. However, to date, wild diversity is only poorly characterized and evaluated. Banana has a large wild diversity but only a narrow proportion is currently used in breeding programmes. The main objective of this study was to evaluate genotype-dependent transpiration responses in relation to the environment. By applying continuous high-throughput phenotyping, we were able to construct genotype-specific transpiration response models in relation to light, VPD and soil water potential. We characterized and evaluated six (sub)species and discerned four phenotypic clusters. Significant differences were observed in leaf area, cumulative transpiration and transpiration efficiency. We confirmed a general stomatal-driven 'isohydric' drought avoidance behaviour, but discovered genotypic differences in the onset and intensity of stomatal closure. We pinpointed crucial genotype-specific soil water potentials when drought avoidance mechanisms were initiated and when stress kicked in. Differences between (sub)species were dependent on environmental conditions, illustrating the need for high-throughput dynamic phenotyping, modelling and validation. We conclude that the banana wild relatives contain useful drought tolerance traits, emphasising the importance of their conservation and potential for use in breeding programmes.
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Affiliation(s)
- David Eyland
- Laboratory of Tropical Crop Improvement, Division of Crop BiotechnicsKU LeuvenLeuvenBelgium
| | - Nathalie Luchaire
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Llorenç Cabrera‐Bosquet
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Boris Parent
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Steven B. Janssens
- Department ResearchMeise Botanic GardenMeiseBelgium
- Department of BiologyKU LeuvenLeuvenBelgium
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Division of Crop BiotechnicsKU LeuvenLeuvenBelgium
- Banana and Plantain Crop ImprovementInternational Institute of Tropical AgricultureKampalaUganda
| | - Claude Welcker
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - François Tardieu
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Sebastien C. Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop BiotechnicsKU LeuvenLeuvenBelgium
- Biodiversity for Food and AgricultureBioversity InternationalLeuvenBelgium
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76
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Mohd Saad NS, Neik TX, Thomas WJW, Amas JC, Cantila AY, Craig RJ, Edwards D, Batley J. Advancing designer crops for climate resilience through an integrated genomics approach. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102220. [PMID: 35489163 DOI: 10.1016/j.pbi.2022.102220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 03/15/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Climate change and exponential population growth are exposing an immediate need for developing future crops that are highly resilient and adaptable to changing environments to maintain global food security in the next decade. Rigorous selection from long domestication history has rendered cultivated crops genetically disadvantaged, raising concerns in their ability to adapt to these new challenges and limiting their usefulness in breeding programmes. As a result, future crop improvement efforts must rely on integrating various genomic strategies ranging from high-throughput sequencing to machine learning, in order to exploit germplasm diversity and overcome bottlenecks created by domestication, expansive multi-dimensional phenotypes, arduous breeding processes, complex traits and big data.
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Affiliation(s)
- Nur Shuhadah Mohd Saad
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ting Xiang Neik
- Sunway College Kuala Lumpur, Bandar Sunway, 47500, Selangor, Malaysia
| | - William J W Thomas
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Junrey C Amas
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Aldrin Y Cantila
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ryan J Craig
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
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Klimova A, Ruiz Mondragón KY, Molina Freaner F, Aguirre-Planter E, Eguiarte LE. Genomic Analyses of Wild and Cultivated Bacanora Agave (Agave angustifolia var. pacifica) Reveal Inbreeding, Few Signs of Cultivation History and Shallow Population Structure. PLANTS 2022; 11:plants11111426. [PMID: 35684199 PMCID: PMC9183054 DOI: 10.3390/plants11111426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 01/12/2023]
Abstract
Due to the recent increase in demand for agave-based beverages, many wild agave populations have experienced rapid decline and fragmentation, whereas cultivated plants are now managed at monocultural plantations, in some cases involving clonal propagation. We examined the relative effect of migration, genetic drift, natural selection and human activities on the genetic repertoire of Agave angustifolia var. pacifica, an agave used for bacanora (an alcoholic spirit similar to tequila) production in northwestern Mexico. We sampled 34 wild and cultivated sites and used over eleven thousand genome-wide SNPs. We found shallow genetic structure among wild samples, although we detected differentiation between coastal and inland sites. Surprisingly, no differentiation was found between cultivated and wild populations. Moreover, we detected moderate inbreeding (FIS ~ 0.13) and similar levels of genomic diversity in wild and cultivated agaves. Nevertheless, the cultivated plants had almost no private alleles and presented evidence of clonality. The overall low genetic structure in A. angustifolia var. pacifica is apparently the result of high dispersibility promoted by pollinators and the possibility of clonal reproduction. Incipient cultivation history and reliance on wild seeds and plants are probably responsible for the observed patterns of high genetic connectivity and considerable diversity in cultivated samples.
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Affiliation(s)
- Anastasia Klimova
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n Annex to the Botanical Garden, Mexico City 04510, Mexico; (K.Y.R.M.); (E.A.-P.)
- Correspondence: (A.K.); (L.E.E.); Tel.: +052-6121716113 (A.K.); +052-5556229006 (L.E.E.)
| | - Karen Y. Ruiz Mondragón
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n Annex to the Botanical Garden, Mexico City 04510, Mexico; (K.Y.R.M.); (E.A.-P.)
| | - Francisco Molina Freaner
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México Hermosillo, Sonora 83250, Mexico;
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n Annex to the Botanical Garden, Mexico City 04510, Mexico; (K.Y.R.M.); (E.A.-P.)
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n Annex to the Botanical Garden, Mexico City 04510, Mexico; (K.Y.R.M.); (E.A.-P.)
- Correspondence: (A.K.); (L.E.E.); Tel.: +052-6121716113 (A.K.); +052-5556229006 (L.E.E.)
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Abdullah M, Okemo P, Furtado A, Henry R. Potential of Genome Editing to Capture Diversity From Australian Wild Rice Relatives. Front Genome Ed 2022; 4:875243. [PMID: 35572739 PMCID: PMC9091330 DOI: 10.3389/fgeed.2022.875243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Rice, a staple food worldwide and a model crop, could benefit from the introduction of novel genetics from wild relatives. Wild rice in the AA genome group closely related to domesticated rice is found across the tropical world. Due to their locality outside the range of domesticated rice, Australian wild rice populations are a potential source of unique traits for rice breeding. These rice species provide a diverse gene pool for improvement that could be utilized for desirable traits such as stress resistance, disease tolerance, and nutritional qualities. However, they remain poorly characterized. The CRISPR/Cas system has revolutionized gene editing and has improved our understanding of gene functions. Coupled with the increasing availability of genomic information on the species, genes in Australian wild rice could be modified through genome editing technologies to produce new domesticates. Alternatively, beneficial alleles from these rice species could be incorporated into cultivated rice to improve critical traits. Here, we summarize the beneficial traits in Australian wild rice, the available genomic information and the potential of gene editing to discover and understand the functions of novel alleles. Moreover, we discuss the potential domestication of these wild rice species for health and economic benefits to rice production globally.
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Affiliation(s)
- Muhammad Abdullah
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
- ARC Centre for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, Australia
| | - Pauline Okemo
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
- ARC Centre for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
- ARC Centre for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Robert Henry,
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Chang CW, Fridman E, Mascher M, Himmelbach A, Schmid K. Physical geography, isolation by distance and environmental variables shape genomic variation of wild barley (Hordeum vulgare L. ssp. spontaneum) in the Southern Levant. Heredity (Edinb) 2022; 128:107-119. [PMID: 35017679 PMCID: PMC8814169 DOI: 10.1038/s41437-021-00494-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 01/12/2023] Open
Abstract
Determining the extent of genetic variation that reflects local adaptation in crop-wild relatives is of interest for the purpose of identifying useful genetic diversity for plant breeding. We investigated the association of genomic variation with geographical and environmental factors in wild barley (Hordeum vulgare L. ssp. spontaneum) populations of the Southern Levant using genotyping by sequencing (GBS) of 244 accessions in the Barley 1K+ collection. The inference of population structure resulted in four genetic clusters that corresponded to eco-geographical habitats and a significant association between lower gene flow rates and geographical barriers, e.g. the Judaean Mountains and the Sea of Galilee. Redundancy analysis (RDA) revealed that spatial autocorrelation explained 45% and environmental variables explained 15% of total genomic variation. Only 4.5% of genomic variation was solely attributed to environmental variation if the component confounded with spatial autocorrelation was excluded. A synthetic environmental variable combining latitude, solar radiation, and accumulated precipitation explained the highest proportion of genomic variation (3.9%). When conditioned on population structure, soil water capacity was the most important environmental variable explaining 1.18% of genomic variation. Genome scans with outlier analysis and genome-environment association studies were conducted to identify adaptation signatures. RDA and outlier methods jointly detected selection signatures in the pericentromeric regions, which have reduced recombination, of the chromosomes 3H, 4H, and 5H. However, selection signatures mostly disappeared after correction for population structure. In conclusion, adaptation to the highly diverse environments of the Southern Levant over short geographical ranges had a limited effect on the genomic diversity of wild barley. This highlighted the importance of nonselective forces in genetic differentiation.
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Affiliation(s)
| | - Eyal Fridman
- Plant Sciences Institute, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Germany
| | - Karl Schmid
- University of Hohenheim, Stuttgart, Germany.
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Cortés AJ, Cornille A, Yockteng R. Evolutionary Genetics of Crop-Wild Complexes. Genes (Basel) 2021; 13:1. [PMID: 35052346 PMCID: PMC8774885 DOI: 10.3390/genes13010001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022] Open
Abstract
Since Darwin's time, the role of crop wild relatives (CWR), landraces, and cultivated genepools in shaping plant diversity and boosting food resources has been a major question [...].
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 vía Rionegro—Las Palmas, Rionegro 054048, Colombia
- Facultad de Ciencias Agrarias—Departamento de Ciencias Forestales, Universidad Nacional de Colombia—Sede Medellín, Medellín 050034, Colombia
| | - Amandine Cornille
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Gif-sur-Yvette, France; or
| | - Roxana Yockteng
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. Tibaitatá, Km 14 vía Mosquera, Cundinamarca 250047, Colombia;
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, National Museum of Natural History, 75005 Paris, France
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Varshney RK. The Plant Genome special issue: Advances in genomic selection and application of machine learning in genomic prediction for crop improvement. THE PLANT GENOME 2021; 14:e20178. [PMID: 34806845 DOI: 10.1002/tpg2.20178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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