Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics
International Crops Research Institute for the Semi-Arid Tropics1, United States Department of Agriculture2, Indian Institute of Pulses Research3, Egerton University4, Agricultural Research Organization, Volcani Center5, Indian Agricultural Research Institute6, Jawaharlal Nehru Agricultural University7, Mahatma Phule Krishi Vidyapeeth8, University of Agricultural Sciences, Dharwad9, Crops Research Institute10
TL;DR: The use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries is proposed.
About: This article is published in Biotechnology Advances.The article was published on 2013-12-01 and is currently open access. It has received 278 citations till now. The article focuses on the topics: Molecular breeding.
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28 Jan 2021
TL;DR: In this paper, the authors have discussed the sophisticated adaptation mechanisms and regularity network that improves the water stress tolerance and adaptation in plants, including growth pattern and structural dynamics, reduction in transpiration loss through altering stomatal conductance and distribution, leaf rolling, root-to-shoot ratio dynamics, root length increment, accumulation of compatible solutes, enhancement of transpiration efficiency, osmotic and hormonal regulation, and delayed senescence.
Abstract: Drought stress, being the inevitable factor that exists in various environments without recognizing borders and no clear warning thereby hampering plant biomass production, quality, and energy. It is the key important environmental stress that occurs due to temperature dynamics, light intensity, and low rainfall. Despite this, its cumulative, not obvious impact and multidimensional nature severely affects the plant morphological, physiological, biochemical and molecular attributes with adverse impact on photosynthetic capacity. Coping with water scarcity, plants evolve various complex resistance and adaptation mechanisms including physiological and biochemical responses, which differ with species level. The sophisticated adaptation mechanisms and regularity network that improves the water stress tolerance and adaptation in plants are briefly discussed. Growth pattern and structural dynamics, reduction in transpiration loss through altering stomatal conductance and distribution, leaf rolling, root to shoot ratio dynamics, root length increment, accumulation of compatible solutes, enhancement in transpiration efficiency, osmotic and hormonal regulation, and delayed senescence are the strategies that are adopted by plants under water deficit. Approaches for drought stress alleviations are breeding strategies, molecular and genomics perspectives with special emphasis on the omics technology alteration i.e., metabolomics, proteomics, genomics, transcriptomics, glyomics and phenomics that improve the stress tolerance in plants. For drought stress induction, seed priming, growth hormones, osmoprotectants, silicon (Si), selenium (Se) and potassium application are worth using under drought stress conditions in plants. In addition, drought adaptation through microbes, hydrogel, nanoparticles applications and metabolic engineering techniques that regulate the antioxidant enzymes activity for adaptation to drought stress in plants, enhancing plant tolerance through maintenance in cell homeostasis and ameliorates the adverse effects of water stress are of great potential in agriculture.
324 citations
TL;DR: Two parallel marker‐assisted backcrossing programs by targeting foc1 locus and two quantitative trait loci regions, ABQTL‐I and ABQ TL‐II, were undertaken to introgress resistance to FW and AB, respectively, in C 214, an elite cultivar of chickpea.
Abstract: Fusarium wilt (FW) and Ascochyta blight (AB) are two major constraints to chickpea (Cicer arietinum L.) production. Therefore, two parallel marker-assisted backcrossing (MABC) programs by targeting foc1 locus and two quantitative trait loci (QTL) regions, ABQTL-I and ABQTL-II, were undertaken to introgress resistance to FW and AB, respectively, in C 214, an elite cultivar of chickpea. In the case of FW, foreground selection (FGS) was conducted with six markers (TR19, TA194, TAA60, GA16, TA110, and TS82) linked to foc1 in the cross C 214 × WR 315 (FWresistant). On the other hand, eight markers (TA194, TR58, TS82, GA16, SCY17, TA130, TA2, and GAA47) linked with ABQTL-I and ABQTL-II were used in the case of AB by deploying C 214 × ILC 3279 (AB-resistant) cross. Background selection (BGS) in both crosses was employed with evenly distributed 40 (C 214 × WR 315) to 43 (C 214 × ILC 3279) SSR markers in the chickpea genome to select plant(s) with higher recurrent parent genome (RPG) recovery. By using three backcrosses and three rounds of selfing, 22 BC 3F4 lines were generated for C 214 × WR 315 cross and 14 MABC lines for C 214 × ILC 3279 cross. Phenotyping of these lines has identified three resistant lines (with 92.7–95.2% RPG) to race 1 of FW, and seven resistant lines (with 81.7–85.40% RPG) to AB that may be tested for yield and other agronomic traits under multilocation trials for possible release and cultivation.
263 citations
Bidhan Chandra Krishi Viswavidyalaya1, University of Queensland2, International Institute of Tropical Agriculture3, China Agricultural University4, Murdoch University5, University of Alabama in Huntsville6, University of Wisconsin-Madison7, University of California, Davis8, University of Tsukuba9, Aberystwyth University10, International Rice Research Institute11, University of Nottingham12, University of Missouri13, Grains Research and Development Corporation14, Swedish University of Agricultural Sciences15, University of Georgia16, International Crops Research Institute for the Semi-Arid Tropics17, Oak Ridge National Laboratory18
TL;DR: The present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
Abstract: Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
231 citations
Cites background from "Achievements and prospects of genom..."
...The draft genome sequence of both Kabuli (http://www. icrisat.org/gt-bt/ICGGC/GenomeSequencing.htm) and Desi (http://www.nipgr.res.in/CGWR/home.php) chickpeas have recently been published (Jain et al., 2013; Varshney et al., 2013b)....
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...To overcome these production constraints and meet the growing demand for these crops, efforts at national and international levels have led to the development of large-scale genetic and genomic resources (Varshney et al., 2013a)....
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TL;DR: These validated and highly informative GKAMs may be useful for genetics and breeding applications in Arachis species and are screened on 280 diverse genotypes of the reference set for estimating diversity features and elucidating genetic relationships.
Abstract: Kompetitive allele-specific polymerase chain reaction (KASP) assays have emerged as cost-effective marker assays especially for molecular breeding applications. Therefore, a set of 96 informative single nucleotide polymorphisms (SNPs) was used to develop KASP assays in groundnut or peanut (Arachis spp.). Developed assays were designated as groundnut KASP assay markers (GKAMs) and screened on 94 genotypes (validation set) that included parental lines of 27 mapping populations, seven synthetic autotetraploid and amphidiploid lines, and 19 wild species accessions. As a result, 90 GKAMs could be validated and 73 GKAMs showed polymorphism in the validation set. Validated GKAMs were screened on 280 diverse genotypes of the reference set for estimating diversity features and elucidating genetic relationships. Cluster analysis of marker allelic data grouped accessions according to their genome type, subspecies, and botanical variety. The subspecies Arachis hypogaea L. subsp. fastigiata Waldron and A. hypogaea subsp. hypogaea formed distinct cluster; however, some overlaps were found indicating their frequent intercrossing during the course of evolution. The wild species, having diploid genomes, were grouped into a single cluster. The average polymorphism information content value for polymorphic GKAMs was 0.32 in the validation set and 0.31 in the reference set. These validated and highly informative GKAMs may be useful for genetics and breeding applications in Arachis species. P
222 citations
TL;DR: An overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries is provided.
Abstract: Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gain is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last five years. The availability of draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seem appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries.
164 citations
Cites background or methods from "Achievements and prospects of genom..."
...Further availability of linked markers in future from trait mapping pipeline will provide more options to the breeders in accumulating favorable alleles for multiple traits in a single genetic background using MABC approach....
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...The MABC has been the most preferred and result oriented molecular breeding approach for improving existing popular genotypes for one or two traits and pyramiding of few genes/QTLs....
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...In the case of chickpea, MABC has been successfully used for introgressing a “QTL-hotspot” harboring several QTLs controlling several drought tolerance related root traits in the elite chickpea variety JG 11 (drought tolerant variety; Varshney et al., 2013a)....
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...Such markers are prerequisite for deploying MAS, MABC, and MARS in crops....
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...Recently, MutMap approach has been found useful in identifying candidate gene for salinity tolerance leading to development of salt tolerance line through MABC (Takagi et al., 2015)....
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References
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University of Tennessee1, Oak Ridge National Laboratory2, West Virginia University3, Umeå University4, University of British Columbia5, United States Department of Energy6, Ghent University7, Swedish University of Agricultural Sciences8, Institut national de la recherche agronomique9, Virginia Tech10, Michigan Technological University11, University of Toronto12, Pennsylvania State University13, University of Provence14, University of Georgia15, University of Florida16, University of California, Berkeley17, Lawrence Berkeley National Laboratory18, University of Arizona19, Purdue University20, Stanford University21, United States Department of Agriculture22, University of Helsinki23, University of Turku24, Massachusetts Institute of Technology25, University of Tennessee Health Science Center26, University of Tübingen27
TL;DR: The draft genome of the black cottonwood tree, Populus trichocarpa, has been reported in this paper, with more than 45,000 putative protein-coding genes identified.
Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
4,025 citations
Agricultural Research Service1, University of North Carolina at Charlotte2, Purdue University3, University of California, Berkeley4, University of Arizona5, University of Maryland, College Park6, University of Missouri7, Joint Genome Institute8, National Center for Genome Resources9, Iowa State University10, University of Wisconsin–Stevens Point11, University of Nebraska–Lincoln12
TL;DR: An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.
Abstract: Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.
3,743 citations
Additional excerpts
...…such as those from cucumber (26,682; Huang et al., 2009), cacao (28,798; Argout et al., 2011), grapevine (29,585; Jaillon et al., 2007) and lotus (38,483), but it is comparable to poplar (45,555; Tuskan et al., 2006), soybean (46,430; Schmutz et al., 2010) andmedicago (47,529; Young et al., 2011)....
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..., 2006), soybean (46,430; Schmutz et al., 2010) andmedicago (47,529; Young et al....
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TL;DR: A high-quality draft of the genome sequence of grapevine is obtained from a highly homozygous genotype, revealing the contribution of three ancestral genomes to the grapevine haploid content and explaining the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
Abstract: The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
3,311 citations
"Achievements and prospects of genom..." refers background in this paper
..., 2011), grapevine (29,585; Jaillon et al., 2007) and lotus (38,483), but it is comparable to poplar (45,555; Tuskan et al....
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...…to other sequenced plant genomes, such as those from cucumber (26,682; Huang et al., 2009), cacao (28,798; Argout et al., 2011), grapevine (29,585; Jaillon et al., 2007) and lotus (38,483), but it is comparable to poplar (45,555; Tuskan et al., 2006), soybean (46,430; Schmutz et al., 2010)…...
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TL;DR: This survey identified several horticultural crops in a variety of families with genomes only two or three times as large asArabidopsis and several fruit trees (a pricot, cherry, mango, orange, papaya, and peach) that should facilitate molecular studies of these crops.
Abstract: Nuclear DNA contents of more than 100 important plant species were measured by flow cytometry of isolated nuclei stained with propidium iodide.Arabidopsis exhibits developmentally regulated multiploidy and has a 2C nuclear DNA content of 0.30 pg (145 Mbp/1C), twice the value usually cited. The 2C value for rice is only about three times that ofArabidopsis. Tomato has a 2C value of about 2.0 pg, larger than commonly cited. This survey identified several horticultural crops in a variety of families with genomes only two or three times as large asArabidopsis; these include several fruit trees (a pricot, cherry, mango, orange, papaya, and peach). The small genome sizes of rice and the horticultural plants should facilitate molecular studies of these crops.
2,930 citations
"Achievements and prospects of genom..." refers background in this paper
...Chickpea, also known as garbanzo bean, is a self-pollinated diploid (2n=2×=16) crop with genome size of 740 Mb (Arumuganathan and Earle, 1991)....
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University of Southern Denmark1, University of Minnesota2, Beijing Normal University3, China Agricultural University4, Boyce Thompson Institute for Plant Research5, University of Wisconsin-Madison6, Wageningen University and Research Centre7, Chinese Academy of Sciences8, Renmin University of China9, Gyeongsang National University10, Aarhus University11, University of Copenhagen12, South China University of Technology13
TL;DR: This study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo, and identifies 686 gene clusters related to phloem function.
Abstract: Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and 'fresh green' odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system.
1,289 citations
"Achievements and prospects of genom..." refers background in this paper
...…revealed that the number of predicted genes in the pigeonpea genome is higher to other sequenced plant genomes, such as those from cucumber (26,682; Huang et al., 2009), cacao (28,798; Argout et al., 2011), grapevine (29,585; Jaillon et al., 2007) and lotus (38,483), but it is comparable to poplar…...
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...Comparative analysis revealed that the number of predicted genes in the pigeonpea genome is higher to other sequenced plant genomes, such as those from cucumber (26,682; Huang et al., 2009), cacao (28,798; Argout et al....
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