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Kapoor C, Anamika, Mukesh Sankar S, Singh SP, Singh N, Kumar S. Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet. PLANTA 2024; 259:155. [PMID: 38750378 DOI: 10.1007/s00425-024-04423-0] [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: 12/17/2023] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.
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Affiliation(s)
- Chandan Kapoor
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Anamika
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Mukesh Sankar
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - S P Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nirupma Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sudhir Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Angelakopoulos R, Tsipourlianos A, Giannoulis T, Mamuris Z, Moutou KA. MassArray Genotyping as a Selection Tool for Extending the Shelf-Life of Fresh Gilthead Sea Bream and European Seabass. Animals (Basel) 2024; 14:205. [PMID: 38254374 PMCID: PMC10812826 DOI: 10.3390/ani14020205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/12/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
In modern aquaculture, genomics-driven breeding programs have emerged as powerful tools for optimizing fish quality. This study focused on two emblematic Mediterranean fish species, the European seabass (Dicentrarchus labrax) and the gilthead sea bream (Sparus aurata), with a primary aim of exploring the genetic basis of white muscle/fillet degradation in fresh fish following harvest. We identified 57 and 44 missense SNPs in gilthead sea bream and European seabass, respectively, located within genes encoding for endogenous proteases responsible for fillet quality. These SNPs were cherry-picked based on their strategic location within the catalytic/regulatory domains of endogenous proteases that are expressed in the white muscle. Using MassArray technology, we successfully associated differentiated enzymatic activity of those endogenous proteases post-harvest as a phenotypic trait with genetic polymorphism of six SNPs in gilthead sea bream and nine in European seabass. These findings can be valuable attributes in selective breeding programs toward the extension of freshness and shelf life of these species. The integration of MassArray technology into breeding programs offers a cost-effective strategy for harnessing the potential of these genetic variants to enhance the overall quality of the final product. Recognizing that fresh fish perishability is a challenge, extending shelf-life is pivotal in reducing losses and production costs.
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Affiliation(s)
- Rafael Angelakopoulos
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Andreas Tsipourlianos
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Science, University of Thessaly, Greece Gaiopolis, 41334 Larissa, Greece;
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Katerina A. Moutou
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
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3
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Rahman MW, Deokar AA, Lindsay D, Tar’an B. Novel Alleles from Cicer reticulatum L. for Genetic Improvement of Cultivated Chickpeas Identified through Genome Wide Association Analysis. Int J Mol Sci 2024; 25:648. [PMID: 38203819 PMCID: PMC10779240 DOI: 10.3390/ijms25010648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/24/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024] Open
Abstract
The availability of wild chickpea (Cicer reticulatum L.) accessions has the potential to be used for the improvement of important traits in cultivated chickpeas. The main objectives of this study were to evaluate the phenotypic and genetic variations of chickpea progeny derived from interspecific crosses between C. arietinum and C. reticulatum, and to establish the association between single nucleotide polymorphism (SNP) markers and a series of important agronomic traits in chickpea. A total of 486 lines derived from interspecific crosses between C. arietinum (CDC Leader) and 20 accessions of C. reticulatum were evaluated at different locations in Saskatchewan, Canada in 2017 and 2018. Significant variations were observed for seed weight per plant, number of seeds per plant, thousand seed weight, and plant biomass. Path coefficient analysis showed significant positive direct effects of the number of seeds per plant, thousand seed weight, and biomass on the total seed weight. Cluster analysis based on the agronomic traits generated six groups that allowed the identification of potential heterotic groups within the interspecific lines for yield improvement and resistance to ascochyta blight disease. Genotyping of the 381 interspecific lines using a modified genotyping by sequencing (tGBS) generated a total of 14,591 SNPs. Neighbour-joining cluster analysis using the SNP data grouped the lines into 20 clusters. The genome wide association analysis identified 51 SNPs that had significant associations with different traits. Several candidate genes associated with early flowering and yield components were identified. The candidate genes and the significant SNP markers associated with different traits have a potential to aid the trait introgression in the breeding program.
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Affiliation(s)
| | | | | | - Bunyamin Tar’an
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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4
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Gepts P. Biocultural diversity and crop improvement. Emerg Top Life Sci 2023; 7:ETLS20230067. [PMID: 38084755 PMCID: PMC10754339 DOI: 10.1042/etls20230067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Biocultural diversity is the ever-evolving and irreplaceable sum total of all living organisms inhabiting the Earth. It plays a significant role in sustainable productivity and ecosystem services that benefit humanity and is closely allied with human cultural diversity. Despite its essentiality, biodiversity is seriously threatened by the insatiable and inequitable human exploitation of the Earth's resources. One of the benefits of biodiversity is its utilization in crop improvement, including cropping improvement (agronomic cultivation practices) and genetic improvement (plant breeding). Crop improvement has tended to decrease agricultural biodiversity since the origins of agriculture, but awareness of this situation can reverse this negative trend. Cropping improvement can strive to use more diverse cultivars and a broader complement of crops on farms and in landscapes. It can also focus on underutilized crops, including legumes. Genetic improvement can access a broader range of biodiversity sources and, with the assistance of modern breeding tools like genomics, can facilitate the introduction of additional characteristics that improve yield, mitigate environmental stresses, and restore, at least partially, lost crop biodiversity. The current legal framework covering biodiversity includes national intellectual property and international treaty instruments, which have tended to limit access and innovation to biodiversity. A global system of access and benefit sharing, encompassing digital sequence information, would benefit humanity but remains an elusive goal. The Kunming-Montréal Global Biodiversity Framework sets forth an ambitious set of targets and goals to be accomplished by 2030 and 2050, respectively, to protect and restore biocultural diversity, including agrobiodiversity.
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Affiliation(s)
- Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95616-8780, U.S.A
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5
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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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6
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Singh G, Gudi S, Amandeep, Upadhyay P, Shekhawat PK, Nayak G, Goyal L, Kumar D, Kumar P, Kamboj A, Thada A, Shekhar S, Koli GK, DP M, Halladakeri P, Kaur R, Kumar S, Saini P, Singh I, Ayoubi H. Unlocking the hidden variation from wild repository for accelerating genetic gain in legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:1035878. [PMID: 36438090 PMCID: PMC9682257 DOI: 10.3389/fpls.2022.1035878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 11/02/2023]
Abstract
The fluctuating climates, rising human population, and deteriorating arable lands necessitate sustainable crops to fulfil global food requirements. In the countryside, legumes with intriguing but enigmatic nitrogen-fixing abilities and thriving in harsh climatic conditions promise future food security. However, breaking the yield plateau and achieving higher genetic gain are the unsolved problems of legume improvement. Present study gives emphasis on 15 important legume crops, i.e., chickpea, pigeonpea, soybean, groundnut, lentil, common bean, faba bean, cowpea, lupin, pea, green gram, back gram, horse gram, moth bean, rice bean, and some forage legumes. We have given an overview of the world and India's area, production, and productivity trends for all legume crops from 1961 to 2020. Our review article investigates the importance of gene pools and wild relatives in broadening the genetic base of legumes through pre-breeding and alien gene introgression. We have also discussed the importance of integrating genomics, phenomics, speed breeding, genetic engineering and genome editing tools in legume improvement programmes. Overall, legume breeding may undergo a paradigm shift once genomics and conventional breeding are integrated in the near future.
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Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Upadhyay
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pooja Kanwar Shekhawat
- Division of Crop Improvement, Plant Breeding and Genetics, Indian Council of Agricultural Research (ICAR)-Central Soil Salinity Research Institute, Karnal, Haryana, India
- Department of Plant Breeding and Genetics, Sri Karan Narendra Agriculture University, Jobner, Rajasthan, India
| | - Gyanisha Nayak
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Lakshay Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Deepak Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Akashdeep Kamboj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Shweta Shekhar
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ganesh Kumar Koli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Meghana DP
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Anand, Gujarat, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Sumit Kumar
- Department of Agronomy, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pawan Saini
- CSB-Central Sericultural Research & Training Institute (CSR&TI), Ministry of Textiles, Govt. of India, Jammu- Kashmir, Pampore, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Habiburahman Ayoubi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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7
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Zurn JD, Hummer KE, Bassil NV. Exploring the diversity and genetic structure of the U.S. National Cultivated Strawberry Collection. HORTICULTURE RESEARCH 2022; 9:uhac125. [PMID: 35928399 PMCID: PMC9343918 DOI: 10.1093/hr/uhac125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The cultivated strawberry (Fragaria ×ananassa) arose through a hybridization of two wild American octoploid strawberry species in a French garden in the 1750s. Since then, breeders have developed improved cultivars adapted to different growing regions. Diverse germplasm is crucial to meet the challenges strawberry breeders will continue to address. The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon maintains the U.S. strawberry collection. Recent developments in high-throughput genotyping for strawberry can provide new insights about the diversity and structure of the collection, germplasm management, and future breeding strategies. Genotyping was conducted on 539 F. ×ananassa accessions using either the iStraw35 or FanaSNP 50 K Axiom array. Data for markers shared by the two arrays were curated for call quality, missing data, and minor allele frequency resulting in 4033 markers for structure assessment, diversity analysis, pedigree confirmation, core collection development, and the identification of haplotypes associated with desirable traits. The F. ×ananassa collection was equally diverse across the different geographic regions represented. K-means clustering, sNMF, and UPGMA hierarchal clustering revealed seven to nine sub-populations associated with different geographic breeding centers. Two 100 accession core collections were created. Pedigree linkages within the collection were confirmed. Finally, accessions containing disease resistance-associated haplotypes for FaRCa1, FaRCg1, FaRMp1, and FaRPc2 were identified. These new core collections will allow breeders and researchers to more efficiently utilize the F. ×ananassa collection. The core collections and other accessions of interest can be requested for research from the USDA-ARS NCGR via the Germplasm Resources Information Network (https://www.ars-grin.gov/).
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Affiliation(s)
- Jason D Zurn
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
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8
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Parihar AK, Kumar J, Gupta DS, Lamichaney A, Naik SJ S, Singh AK, Dixit GP, Gupta S, Toklu F. Genomics Enabled Breeding Strategies for Major Biotic Stresses in Pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:861191. [PMID: 35665148 PMCID: PMC9158573 DOI: 10.3389/fpls.2022.861191] [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: 01/24/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Pea (Pisum sativum L.) is one of the most important and productive cool season pulse crops grown throughout the world. Biotic stresses are the crucial constraints in harnessing the potential productivity of pea and warrant dedicated research and developmental efforts to utilize omics resources and advanced breeding techniques to assist rapid and timely development of high-yielding multiple stress-tolerant-resistant varieties. Recently, the pea researcher's community has made notable achievements in conventional and molecular breeding to accelerate its genetic gain. Several quantitative trait loci (QTLs) or markers associated with genes controlling resistance for fusarium wilt, fusarium root rot, powdery mildew, ascochyta blight, rust, common root rot, broomrape, pea enation, and pea seed borne mosaic virus are available for the marker-assisted breeding. The advanced genomic tools such as the availability of comprehensive genetic maps and linked reliable DNA markers hold great promise toward the introgression of resistance genes from different sources to speed up the genetic gain in pea. This review provides a brief account of the achievements made in the recent past regarding genetic and genomic resources' development, inheritance of genes controlling various biotic stress responses and genes controlling pathogenesis in disease causing organisms, genes/QTLs mapping, and transcriptomic and proteomic advances. Moreover, the emerging new breeding approaches such as transgenics, genome editing, genomic selection, epigenetic breeding, and speed breeding hold great promise to transform pea breeding. Overall, the judicious amalgamation of conventional and modern omics-enabled breeding strategies will augment the genetic gain and could hasten the development of biotic stress-resistant cultivars to sustain pea production under changing climate. The present review encompasses at one platform the research accomplishment made so far in pea improvement with respect to major biotic stresses and the way forward to enhance pea productivity through advanced genomic tools and technologies.
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Affiliation(s)
- Ashok Kumar Parihar
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Jitendra Kumar
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Debjyoti Sen Gupta
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Amrit Lamichaney
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Satheesh Naik SJ
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Anil K. Singh
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Girish P. Dixit
- All India Coordinated Research Project on Chickpea, ICAR-IIPR, Kanpur, India
| | - Sanjeev Gupta
- Indian Council of Agricultural Research, New Delhi, India
| | - Faruk Toklu
- Department of Field Crops, Faculty of Agricultural, Cukurova University, Adana, Turkey
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9
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Sharma S, Schulthess AW, Bassi FM, Badaeva ED, Neumann K, Graner A, Özkan H, Werner P, Knüpffer H, Kilian B. Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm. BIOLOGY 2021; 10:982. [PMID: 34681081 PMCID: PMC8533267 DOI: 10.3390/biology10100982] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 12/02/2022]
Abstract
Wheat (Triticum sp.) is one of the world's most important crops, and constantly increasing its productivity is crucial to the livelihoods of millions of people. However, more than a century of intensive breeding and selection processes have eroded genetic diversity in the elite genepool, making new genetic gains difficult. Therefore, the need to introduce novel genetic diversity into modern wheat has become increasingly important. This review provides an overview of the plant genetic resources (PGR) available for wheat. We describe the most important taxonomic and phylogenetic relationships of these PGR to guide their use in wheat breeding. In addition, we present the status of the use of some of these resources in wheat breeding programs. We propose several introgression schemes that allow the transfer of qualitative and quantitative alleles from PGR into elite germplasm. With this in mind, we propose the use of a stage-gate approach to align the pre-breeding with main breeding programs to meet the needs of breeders, farmers, and end-users. Overall, this review provides a clear starting point to guide the introgression of useful alleles over the next decade.
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Affiliation(s)
- Shivali Sharma
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco;
| | - Ekaterina D. Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia;
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey;
| | - Peter Werner
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
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10
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Mahadevaiah C, Appunu C, Aitken K, Suresha GS, Vignesh P, Mahadeva Swamy HK, Valarmathi R, Hemaprabha G, Alagarasan G, Ram B. Genomic Selection in Sugarcane: Current Status and Future Prospects. FRONTIERS IN PLANT SCIENCE 2021; 12:708233. [PMID: 34646284 PMCID: PMC8502939 DOI: 10.3389/fpls.2021.708233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/24/2021] [Indexed: 05/18/2023]
Abstract
Sugarcane is a C4 and agro-industry-based crop with a high potential for biomass production. It serves as raw material for the production of sugar, ethanol, and electricity. Modern sugarcane varieties are derived from the interspecific and intergeneric hybridization between Saccharum officinarum, Saccharum spontaneum, and other wild relatives. Sugarcane breeding programmes are broadly categorized into germplasm collection and characterization, pre-breeding and genetic base-broadening, and varietal development programmes. The varietal identification through the classic breeding programme requires a minimum of 12-14 years. The precise phenotyping in sugarcane is extremely tedious due to the high propensity of lodging and suckering owing to the influence of environmental factors and crop management practices. This kind of phenotyping requires data from both plant crop and ratoon experiments conducted over locations and seasons. In this review, we explored the feasibility of genomic selection schemes for various breeding programmes in sugarcane. The genetic diversity analysis using genome-wide markers helps in the formation of core set germplasm representing the total genomic diversity present in the Saccharum gene bank. The genome-wide association studies and genomic prediction in the Saccharum gene bank are helpful to identify the complete genomic resources for cane yield, commercial cane sugar, tolerances to biotic and abiotic stresses, and other agronomic traits. The implementation of genomic selection in pre-breeding, genetic base-broadening programmes assist in precise introgression of specific genes and recurrent selection schemes enhance the higher frequency of favorable alleles in the population with a considerable reduction in breeding cycles and population size. The integration of environmental covariates and genomic prediction in multi-environment trials assists in the prediction of varietal performance for different agro-climatic zones. This review also directed its focus on enhancing the genetic gain over time, cost, and resource allocation at various stages of breeding programmes.
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Affiliation(s)
| | - Chinnaswamy Appunu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Karen Aitken
- CSIRO (Commonwealth Scientific and Industrial Research Organization), St. Lucia, QLD, Australia
| | | | - Palanisamy Vignesh
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | | | | | - Govind Hemaprabha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Ganesh Alagarasan
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Bakshi Ram
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
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11
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Solis CA, Yong MT, Venkataraman G, Milham P, Zhou M, Shabala L, Holford P, Shabala S, Chen ZH. Sodium sequestration confers salinity tolerance in an ancestral wild rice. PHYSIOLOGIA PLANTARUM 2021; 172:1594-1608. [PMID: 33619741 DOI: 10.1111/ppl.13352] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 05/27/2023]
Abstract
Wild rice Oryza rufipogon, a progenitor of cultivated rice Oryza sativa L., possesses superior salinity tolerance and is a potential donor for breeding salinity tolerance traits in rice. However, a mechanistic basis of salinity tolerance in this donor species has not been established. Here, we examined salinity tolerance from the early vegetative stage to maturity in O. rufipogon in comparison with a salt-susceptible (Koshihikari) and a salt-tolerant (Reiziq) variety of O. sativa. We assessed their phylogeny and agronomical traits, photosynthetic performance, ion contents, as well as gene expression in response to salinity stress. Salt-tolerant O. rufipogon exhibited efficient leaf photosynthesis and less damage to leaf tissues during the course of salinity treatment. In addition, O. rufipogon showed a significantly higher tissue Na+ accumulation that is achieved by vacuolar sequestration compared to the salt tolerant O. sativa indica subspecies. These findings are further supported by the upregulation of genes involved with ion transport and sequestration (e.g. high affinity K+ transporter 1;4 [HKT1;4], Na+ /H+ exchanger 1 [NHX1] and vacuolar H+ -ATPase c [VHA-c]) in salt-tolerant O. rufipogon as well as by the close phylogenetic relationship of key salt-responsive genes in O. rufipogon to these in salt-tolerant wild rice species such as O. coarctata. Thus, the high accumulation of Na+ in the leaves of O. rufipogon acts as a cheap osmoticum to minimize the high energy cost of osmolyte biosynthesis and excessive reactive oxygen species production. These mechanisms demonstrated that O. rufipogon has important traits that can be used for improving salinity tolerance in cultivated rice.
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Affiliation(s)
- Celymar Angela Solis
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Miing-Tiem Yong
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, M. S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai, India
| | - Paul Milham
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Lana Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
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Egan LM, Hofmann RW, Ghamkhar K, Hoyos-Villegas V. Prospects for Trifolium Improvement Through Germplasm Characterisation and Pre-breeding in New Zealand and Beyond. FRONTIERS IN PLANT SCIENCE 2021; 12:653191. [PMID: 34220882 PMCID: PMC8242581 DOI: 10.3389/fpls.2021.653191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
Trifolium is the most used pastoral legume genus in temperate grassland systems, and a common feature in meadows and open space areas in cities and parks. Breeding of Trifolium spp. for pastoral production has been going on for over a century. However, the breeding targets have changed over the decades in response to different environmental and production pressures. Relatively small gains have been made in Trifolium breeding progress. Trifolium breeding programmes aim to maintain a broad genetic base to maximise variation. New Zealand is a global hub in Trifolium breeding, utilising exotic germplasm imported by the Margot Forde Germplasm Centre. This article describes the history of Trifolium breeding in New Zealand as well as the role and past successes of utilising genebanks in forage breeding. The impact of germplasm characterisation and evaluation in breeding programmes is also discussed. The history and challenges of Trifolium breeding and its effect on genetic gain can be used to inform future pre-breeding decisions in this genus, as well as being a model for other forage legumes.
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Affiliation(s)
- Lucy M. Egan
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Rainer W. Hofmann
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Kioumars Ghamkhar
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Valerio Hoyos-Villegas
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
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Selection of Suitable Potato Genotypes for Late-Sown Heat Stress Conditions Based on Field Performance and Stress Tolerance Indices. SUSTAINABILITY 2021. [DOI: 10.3390/su13052770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
International Potato Center (CIP), -bred potato genotypes produce various yields under heat stress conditions due to being sown late. To explore options for achieving this, a replicated experiment was conducted at the field of Tuber Crops Research Sub-Centre, Bangladesh Agricultural Research Institute, Bogura, Bangladesh to evaluate the performance of fourteen CIP-bred potato genotypes with two controls (Asterix and Granola). The experiment was laid out in a split-plot design with three replications. Several indices were applied to find out the suitable genotypes under heat stress. The plant height increased by 34.61% under heat stress, which was common in all the potato genotypes. Similarly, other yield-participating characters like stem per hill, canopy coverage (%), plant vigor, and tuber number per plant were also increased under heat stress conditions. However, the tuber yield was decreased by 6.30% and 11.41%, respectively when harvested at 70 and 90 days after plantation. Moreover, “CIP-203” yielded the highest (40.66 t ha−1) in non-stressed whereas, “CIP-118” yielded the highest (32.89 t/ha) in stressed conditions. Likewise, the bred “CIP-218” and “CIP-118” performed better under both growing conditions and yielded >35.00 t ha−1. According to a rank-sum test, among the fourteen potato genotypes, “CIP-218”, “LB-7”, “CIP-118”, “CIP-232”, and “CIP-112” were selected as heat-tolerant potatoes and can grow in both growing conditions with higher yield potential.
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Kajiya-Kanegae H, Nagasaki H, Kaga A, Hirano K, Ogiso-Tanaka E, Matsuoka M, Ishimori M, Ishimoto M, Hashiguchi M, Tanaka H, Akashi R, Isobe S, Iwata H. Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections. DNA Res 2021; 28:dsaa032. [PMID: 33492369 PMCID: PMC7934572 DOI: 10.1093/dnares/dsaa032] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/04/2021] [Indexed: 12/11/2022] Open
Abstract
We performed whole-genome Illumina resequencing of 198 accessions to examine the genetic diversity and facilitate the use of soybean genetic resources and identified 10 million single nucleotide polymorphisms and 2.8 million small indels. Furthermore, PacBio resequencing of 10 accessions was performed, and a total of 2,033 structure variants were identified. Genetic diversity and structure analysis congregated the 198 accessions into three subgroups (Primitive, World, and Japan) and showed the possibility of a long and relatively isolated history of cultivated soybean in Japan. Additionally, the skewed regional distribution of variants in the genome, such as higher structural variations on the R gene clusters in the Japan group, suggested the possibility of selective sweeps during domestication or breeding. A genome-wide association study identified both known and novel causal variants on the genes controlling the flowering period. Novel candidate causal variants were also found on genes related to the seed coat colour by aligning together with Illumina and PacBio reads. The genomic sequences and variants obtained in this study have immense potential to provide information for soybean breeding and genetic studies that may uncover novel alleles or genes involved in agronomically important traits.
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Affiliation(s)
- Hiromi Kajiya-Kanegae
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hideki Nagasaki
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Akito Kaga
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Ko Hirano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Eri Ogiso-Tanaka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Motoyuki Ishimori
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Masao Ishimoto
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | | | - Hidenori Tanaka
- Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Ryo Akashi
- Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review. Int J Mol Sci 2020; 21:ijms21249615. [PMID: 33348635 PMCID: PMC7766301 DOI: 10.3390/ijms21249615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Vegetable legumes are an essential source of carbohydrates, vitamins, and minerals, along with health-promoting bioactive chemicals. The demand for the use of either fresh or processed vegetable legumes is continually expanding on account of the growing consumer awareness about their well-balanced diet. Therefore, sustaining optimum yields of vegetable legumes is extremely important. Here we seek to present d etails of prospects of underexploited vegetable legumes for food availability, accessibility, and improved livelihood utilization. So far research attention was mainly focused on pulse legumes' performance as compared to vegetable legumes. Wild and cultivated vegetable legumes vary morphologically across diverse habitats. This could make them less known, underutilized, and underexploited, and make them a promising potential nutritional source in developing nations where malnutrition still exists. Research efforts are required to promote underexploited vegetable legumes, for improving their use to feed the ever-increasing population in the future. In view of all the above points, here we have discussed underexploited vegetable legumes with tremendous potential; namely, vegetable pigeon pea (Cajanus cajan), cluster bean (Cyamopsis tetragonoloba), winged bean (Psophocarpus tetragonolobus), dolichos bean (Lablab purpureus), and cowpea (Vigna unguiculata), thereby covering the progress related to various aspects such as pre-breeding, molecular markers, quantitative trait locus (QTLs), genomics, and genetic engineering. Overall, this review has summarized the information related to advancements in the breeding of vegetable legumes which will ultimately help in ensuring food and nutritional security in developing nations.
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Singh K, Malik S, Gupta S, Chaudhury R. Unlocking genebanks to ensure food and nutrient security and environmental stability. ACTA HORTICULTURAE 2020:1-8. [DOI: 10.17660/actahortic.2020.1297.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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17
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Egan LM, Hofmann RW, Seguin P, Ghamkhar K, Hoyos-Villegas V. Pedigree analysis of pre-breeding efforts in Trifolium spp. germplasm in New Zealand. BMC Genet 2020; 21:104. [PMID: 32928105 PMCID: PMC7489199 DOI: 10.1186/s12863-020-00912-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 08/30/2020] [Indexed: 12/23/2022] Open
Abstract
Background Prebreeding in plants is the activity designed to identify useful characteristics from wild germplasm and its integration in breeding programs. Prebreeding aims to introduce new variation into the populations of a species of interest. Pedigree analysis is a valuable tool for evaluation of variation in genebanks where pedigree maps are used to visualize and describe population structure and variation within these populations. Margot Forde Germplasm Centre (MFGC) is New Zealand’s national forage genebank and holds a collection of ~ 75 species of the genus Trifolium, of which only a dozen have been taken through prebreeding programs. The main objective of this study was to construct pedigree maps and analyse patterns of relatedness for seven minor Trifolium species accessions contained at the MFGC. These species are Trifolium ambiguum, Trifolium arvense, Trifolium dubium, Trifolium hybridum, Trifolium medium, Trifolium subterraneum and the Trifolium repens x Trifolium occidentale interspecific hybrids. We present a history of Trifolium spp. prebreeding in New Zealand and inform breeders of possible alternative forage species to use. Results Pedigree data from accessions introduced between 1950 and 2016 were used and filtered based on breeding activity. Kinship levels among Trifolium spp. remained below 8% and no inbreeding was found. Influential ancestors that contributed largely to populations structure were identified. The Australian cultivar ‘Monaro’ had a strong influence over the whole population of accessions in T. ambiguum. T. subterraneum and T. repens x T. occidentale had the largest number of generations (3). T. ambiguum and T. medium had the highest cumulative kinship across the decades. Conclusions We conclude that there are high levels of diversity in the seven Trifolium spp. studied. However, collection and prebreeding efforts must be strengthened to maximize utilization and bring useful genetic variation.
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Affiliation(s)
- L M Egan
- AgResearch Lincoln Research Centre, Christchurch, PB 4749, New Zealand.,Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - R W Hofmann
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - P Seguin
- Faculty of Agricultural and Environmental Sciences, Department of Plant Science, McGill University, Montreal, Canada
| | - K Ghamkhar
- AgResearch Grassslands Research Centre, Palmerston North, PB 11008, New Zealand
| | - V Hoyos-Villegas
- Faculty of Agricultural and Environmental Sciences, Department of Plant Science, McGill University, Montreal, Canada.
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Guerrero-Zurita F, Ramírez DA, Rinza J, Ninanya J, Blas R, Heider B. Potential Short-Term Memory Induction as a Promising Method for Increasing Drought Tolerance in Sweetpotato Crop Wild Relatives [ Ipomoea series Batatas (Choisy) D. F. Austin]. FRONTIERS IN PLANT SCIENCE 2020; 11:567507. [PMID: 33013990 PMCID: PMC7494806 DOI: 10.3389/fpls.2020.567507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Crop wild relatives of sweetpotato [Ipomoea series Batatas (Choisy) D. F. Austin] are a group of species with potential for use in crop improvement programs seeking to breed for drought tolerance. Stress memory in this group could enhance these species' physiological response to drought, though no studies have yet been conducted in this area. In this pot experiment, drought tolerance, determined using secondary traits, was tested in 59 sweetpotato crop wild relative accessions using potential short-term memory induction. For this purpose, accessions were subjected to two treatments, i) non-priming: full irrigation (up to field capacity, 0.32 w/w) from transplanting to harvest and ii) priming: full irrigation from transplanting to flowering onset (FO) followed by a priming process from FO to harvest. The priming process consisted of three water restriction periods of increasing length (8, 11, and 14 days) followed each by a recovery period of 14 days with full irrigation. Potential stress memory induction was calculated for each accession based on ecophysiological indicators such as senescence, foliar area, leaf-minus-air temperature, and leaf 13C discrimination. Based on total biomass production, resilience and production capacity were calculated per accession to evaluate drought tolerance. Increase in foliar area, efficient leaf thermoregulation, improvement of leaf photosynthetic performance, and delayed senescence were identified in 23.7, 28.8, 50.8, and 81.4% of the total number of accessions, respectively. It was observed that under a severe drought scenario, a resilient response included more long-lived green leaf area while a productive response was related to optimized leaf thermoregulation and gas exchange. Our preliminary results suggest that I. triloba and I. trifida have the potential to improve sweetpotato resilience in dry environments and should be included in introgression breeding programs of this crop. Furthermore, I. splendor-sylvae, I. ramosissima, I. tiliacea, and wild I. batatas were the most productive species studied but given the genetic barriers to interspecific hybridization between these species and sweetpotato, we suggest that further genetic and metabolic studies be conducted on them. Finally, this study proposes a promising method for improving drought tolerance based on potential stress-memory induction, which is applicable both for wild species and crops.
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Affiliation(s)
| | - David A. Ramírez
- Latin American & Caribbean Regional Program, International Potato Center, Lima, Peru
| | - Javier Rinza
- Crop and Systems Science Division, International Potato Center, Lima, Peru
| | - Johan Ninanya
- Crop and Systems Science Division, International Potato Center, Lima, Peru
| | - Raúl Blas
- Crop Husbandry Department, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Bettina Heider
- Genetics, Genomics and Crop Improvement Division, International Potato Center, Lima, Peru
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Al-Farsi SM, Nadaf SK, Al-Sadi AM, Ullah A, Farooq M. Evaluation of indigenous Omani alfalfa landraces for morphology and forage yield under different levels of salt stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1763-1772. [PMID: 32943814 PMCID: PMC7468036 DOI: 10.1007/s12298-020-00856-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/22/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
Alfalfa is the major fodder crop of Sultanate Oman, but salinity is a major problem in its cultivation. Therefore, thirty-four alfalfa (Medicago sativa L.) landraces of Oman were evaluated for morphology and forage yield response to different salinity levels viz. 1 (control), 3, 6, 9, and 12 dS m-1 under greenhouse conditions. The experiment was conducted under a completely randomized design. Different alfalfa landraces responded differently to the five salinity levels for plant height, number of branches, number of leaves, leaflet width, leaflet length, forage fresh weight, and forage dry matter yield. Salt stress caused a reduction in growth and dry matter yield of alfalfa landraces with exception of some, which responded positively to the salinity levels of 3 and 6 dS m-1 compared to control for the number of leaves per plant. Moreover, some landraces had better forage fresh weight and dry matter yield at 6 dS m-1 than 3 dS m-1. Alfalfa landraces OMA 257, OMA, 245, OMA 270, OMA 315, OMA 211, OMA 117, OMA 56, OMA 239, OMA 148, OMA 131, OMA 95, OMA 263, OMA 262, OMA 289 and OMA 220 were designated as salt tolerant based on their overall performance across salinity levels of 6, 9 and 12 dS m-1. However, the landraces OMA 305, OMA 100, OMA 211, OMA 148, OMA 60, OMA 248, OMA 9, OMA 88, and OMA 302 collected were sensitive to 6, 9 and 12 dS m-1 salinity stress. The study showed the variation of alfalfa landraces potential for salinity tolerance, and their potential for cultivation in saline areas and/or use in breeding programs aimed to develop salt tolerant alfalfa genotypes.
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Affiliation(s)
- Safaa Mohammed Al-Farsi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123, Muscat, Oman
- Directorate General of Agriculture and Livestock Research, Ministry of Agriculture and Fisheries, Al-Seeb 121, Muscat, Oman
| | - Saleem K. Nadaf
- Oman Animal and Plant Genetic Resources Center, The Research Council, Muscat, Oman
| | - Abdullah M. Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123, Muscat, Oman
| | - Aman Ullah
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123, Muscat, Oman
| | - Muhammad Farooq
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123, Muscat, Oman
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Sharma S, Paul PJ, Sameer Kumar CV, Nimje C. Utilizing Wild Cajanus platycarpus, a Tertiary Genepool Species for Enriching Variability in the Primary Genepool for Pigeonpea Improvement. FRONTIERS IN PLANT SCIENCE 2020; 11:1055. [PMID: 32793254 PMCID: PMC7390956 DOI: 10.3389/fpls.2020.01055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
The use of crop wild relatives in the breeding program has been well recognized to diversify the genetic base along with introgression of useful traits. Cajanus platycarpus (Benth.) Maesen, an annual wild relative belonging to the tertiary genepool of pigeonpea, possesses many useful traits such as early maturity, high protein content, photoperiod insensitivity, and pod borer tolerance for the genetic improvement of cultivated pigeonpea. Using this cross incompatible wild Cajanus species, an advanced backcross population was developed following the embryo rescue technique. In the present study, a pre-breeding population consisting of 136 introgression lines (ILs) along with five popular varieties (used as checks) was evaluated for important agronomic traits during 2016 and 2017 rainy seasons and for grain nutrient content during 2016, 2017, and 2018 rainy seasons. Large genetic variation was observed for agronomic traits such as days to 50% flowering, number of pods per plant, pod weight per plant, grain yield per plant, and grain nutrients [protein content, grain iron (Fe), zinc (Zn), calcium (Ca), and magnesium (Mg)] in the pre-breeding population. Significant genotype × environment interaction was also observed for agronomic traits as well as grain nutrients indicating the sensitivity of these traits to the environments. No significant correlations were observed between grain yield and grain nutrients except grain Zn content which was negatively correlated with grain yield. Overall, 28 promising high-yielding ILs with high grain nutrient content were identified. These ILs, in particular, ICPP # 171012, 171004, 171102, 171087, 171006, and 171050 flowered significantly earlier than the popular mega variety, ICPL 87119 (Asha) and thus hold potential in developing new short-duration cultivars. The comprehensive multi-site assessment of these high-yielding, nutrient-rich accessions would be useful in identifying region-specific promising lines for direct release as cultivars. Moreover, these ILs are expected to replace the popular existing cultivars or for use as new and diverse sources of variations in hybridization programs for pigeonpea improvement.
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Affiliation(s)
- Shivali Sharma
- Theme Pre-breeding, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pronob J. Paul
- Theme Pre-breeding, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - CV Sameer Kumar
- Regional Agricultural Research Station, Professor Jayashanker Telangana State Agricultural University, Palem, India
| | - Chetna Nimje
- Grain Quality Lab., International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Banla EM, Dzidzienyo DK, Diangar MM, Melomey LD, Offei SK, Tongoona P, Desmae H. Molecular and phenotypic diversity of groundnut ( Arachis hypogaea L.) cultivars in Togo. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1489-1504. [PMID: 32647463 PMCID: PMC7326882 DOI: 10.1007/s12298-020-00837-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/22/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
Diversity assessment of 94 groundnut accessions from Togo and Senegal, using agro-morphological and SNP markers, revealed high variability for many quantitative traits such as late leaf spot (LLS) incidence, number of pods per plant and yield per plant. For qualitative traits, the Simpson Index showed high diversity for primary seed colour (0.75), stem pigmentation (0.60), and Growth habit (0.59). Principal component analysis underscored quantitative traits such as hundred seed weight, days to maturity, and LLS incidence, as the main traits contributing to the divergence. Correlation and path coefficient analysis showed that the number of pods per plant was the main yield-related trait positively affecting yield (r = 0.95, PC = 0.84; p = 0.01). Overall, 990 SNP markers revealed moderate genetic variability in the genotypes and the percentage of heterozygous genotypes varied from 0 to 50% for all loci. Analysis of molecular variance revealed that only 1.1% of the total molecular variance accounted for geographical contribution to the diversity. Co-analysis of phenotypic and SNP data delineated three clusters harbouring useful alleles and interesting phenotypic features such as LLS resistance, large number of pods per plant and early maturity indicating that differences observed at the phenotypic level are underlined by genotypic differences. The phenotypic and genotypic diversity observed could be exploited for the identification of parents with preferred traits for use in the breeding program. However, the low population structure highlights the necessity to improve groundnut diversity in Togo through introduction from various sources.
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Affiliation(s)
- Essohouna Modom Banla
- Institut Togolais de Recherche Agronomique (ITRA), Lomé, Togo
- West Africa Centre for Crop Improvement (WACCI), University of Ghana (UG), PMB 30, Legon, Accra, Ghana
- International Crops Research Institute for the Semi-Arid Tropic (ICRISAT-WCA), BP320, Bamako, Mali
| | - Daniel Kwadjo Dzidzienyo
- West Africa Centre for Crop Improvement (WACCI), University of Ghana (UG), PMB 30, Legon, Accra, Ghana
| | - Mouhamadou Moussa Diangar
- Institut Sénégalais de Recherches Agricoles (ISRA), ISRA CNRA de Bambey, ISRA/Center of Excellence of CERAAS), BP53, Diourbel, Senegal
| | - Leander Dede Melomey
- West Africa Centre for Crop Improvement (WACCI), University of Ghana (UG), PMB 30, Legon, Accra, Ghana
| | - Samuel Kwame Offei
- West Africa Centre for Crop Improvement (WACCI), University of Ghana (UG), PMB 30, Legon, Accra, Ghana
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), University of Ghana (UG), PMB 30, Legon, Accra, Ghana
| | - Haile Desmae
- International Crops Research Institute for the Semi-Arid Tropic (ICRISAT-WCA), BP320, Bamako, Mali
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Solis CA, Yong MT, Vinarao R, Jena K, Holford P, Shabala L, Zhou M, Shabala S, Chen ZH. Back to the Wild: On a Quest for Donors Toward Salinity Tolerant Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:323. [PMID: 32265970 PMCID: PMC7098918 DOI: 10.3389/fpls.2020.00323] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/05/2020] [Indexed: 05/20/2023]
Abstract
Salinity stress affects global food producing areas by limiting both crop growth and yield. Attempts to develop salinity-tolerant rice varieties have had limited success due to the complexity of the salinity tolerance trait, high variation in the stress response and a lack of available donors for candidate genes for cultivated rice. As a result, finding suitable donors of genes and traits for salinity tolerance has become a major bottleneck in breeding for salinity tolerant crops. Twenty-two wild Oryza relatives have been recognized as important genetic resources for quantitatively inherited traits such as resistance and/or tolerance to abiotic and biotic stresses. In this review, we discuss the challenges and opportunities of such an approach by critically analyzing evolutionary, ecological, genetic, and physiological aspects of Oryza species. We argue that the strategy of rice breeding for better Na+ exclusion employed for the last few decades has reached a plateau and cannot deliver any further improvement in salinity tolerance in this species. This calls for a paradigm shift in rice breeding and more efforts toward targeting mechanisms of the tissue tolerance and a better utilization of the potential of wild rice where such traits are already present. We summarize the differences in salinity stress adaptation amongst cultivated and wild Oryza relatives and identify several key traits that should be targeted in future breeding programs. This includes: (1) efficient sequestration of Na+ in mesophyll cell vacuoles, with a strong emphasis on control of tonoplast leak channels; (2) more efficient control of xylem ion loading; (3) efficient cytosolic K+ retention in both root and leaf mesophyll cells; and (4) incorporating Na+ sequestration in trichrome. We conclude that while amongst all wild relatives, O. rufipogon is arguably a best source of germplasm at the moment, genes and traits from the wild relatives, O. coarctata, O. latifolia, and O. alta, should be targeted in future genetic programs to develop salt tolerant cultivated rice.
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Affiliation(s)
- Celymar A. Solis
- School of Science, Western Sydney University, Penrith, NSW, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Miing T. Yong
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Ricky Vinarao
- International Rice Research Institute, Metro Manila, Philippines
| | - Kshirod Jena
- International Rice Research Institute, Metro Manila, Philippines
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Lana Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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23
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van Zonneveld M, Rakha M, Tan SY, Chou YY, Chang CH, Yen JY, Schafleitner R, Nair R, Naito K, Solberg SØ. Mapping patterns of abiotic and biotic stress resilience uncovers conservation gaps and breeding potential of Vigna wild relatives. Sci Rep 2020. [PMID: 32034221 DOI: 10.9755/ejfa.v27i1.17852] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
This study provides insights in patterns of distribution of abiotic and biotic stress resilience across Vigna gene pools to enhance the use and conservation of these genetic resources for legume breeding. Vigna is a pantropical genus with more than 88 taxa including important crops such as V. radiata (mung bean) and V. unguiculata (cowpea). Our results show that sources of pest and disease resistance occur in at least 75 percent of the Vigna taxa, which were part of screening assessments, while sources of abiotic stress resilience occur in less than 30 percent of screened taxa. This difference in levels of resilience suggests that Vigna taxa co-evolve with pests and diseases while taxa are more conservative to adapt to climatic changes and salinization. Twenty-two Vigna taxa are poorly conserved in genebanks or not at all. This germplasm is not available for legume breeding and requires urgent germplasm collecting before these taxa extirpate on farm and in the wild. Vigna taxa, which tolerate heat and drought stress are rare compared with taxa, which escape these stresses because of short growing seasons or with taxa, which tolerate salinity. We recommend prioritizing these rare Vigna taxa for conservation and screening for combined abiotic and biotic stress resilience resulting from stacked or multifunctional traits. The high presence of salinity tolerance compared with drought stress tolerance, suggests that Vigna taxa are good at developing salt-tolerant traits. Vigna taxa are therefore of high value for legume production in areas that will suffer from salinization under global climate change.
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Affiliation(s)
- Maarten van Zonneveld
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan.
| | - Mohamed Rakha
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan
- Horticulture Department, Faculty of Agriculture, University of Kafrelsheikh, Kafr El-Sheikh, 33516, Egypt
| | - Shin Yee Tan
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan
- Univeristi Malaysia Sabah, Batu 10, 90000, Sandakan, Sabah, Malaysia
| | - Yu-Yu Chou
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan
| | - Ching-Huan Chang
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan
| | - Jo-Yi Yen
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan
| | - Roland Schafleitner
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan
| | - Ramakrishnan Nair
- World Vegetable Center, South Asia, ICRISAT Campus, Patancheru, 502324, Hyderabad, Telangana, India
| | - Ken Naito
- Genetic Resources Center, National Agriculture and Food Science Organization, Tsukuba, Ibaraki, Japan
| | - Svein Ø Solberg
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan
- Inland Norway University of Applied Sciences, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, P.O. Box 400, 2418, Elverum, Norway
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24
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van Zonneveld M, Rakha M, Tan SY, Chou YY, Chang CH, Yen JY, Schafleitner R, Nair R, Naito K, Solberg SØ. Mapping patterns of abiotic and biotic stress resilience uncovers conservation gaps and breeding potential of Vigna wild relatives. Sci Rep 2020; 10:2111. [PMID: 32034221 PMCID: PMC7005857 DOI: 10.1038/s41598-020-58646-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 01/14/2020] [Indexed: 11/24/2022] Open
Abstract
This study provides insights in patterns of distribution of abiotic and biotic stress resilience across Vigna gene pools to enhance the use and conservation of these genetic resources for legume breeding. Vigna is a pantropical genus with more than 88 taxa including important crops such as V. radiata (mung bean) and V. unguiculata (cowpea). Our results show that sources of pest and disease resistance occur in at least 75 percent of the Vigna taxa, which were part of screening assessments, while sources of abiotic stress resilience occur in less than 30 percent of screened taxa. This difference in levels of resilience suggests that Vigna taxa co-evolve with pests and diseases while taxa are more conservative to adapt to climatic changes and salinization. Twenty-two Vigna taxa are poorly conserved in genebanks or not at all. This germplasm is not available for legume breeding and requires urgent germplasm collecting before these taxa extirpate on farm and in the wild. Vigna taxa, which tolerate heat and drought stress are rare compared with taxa, which escape these stresses because of short growing seasons or with taxa, which tolerate salinity. We recommend prioritizing these rare Vigna taxa for conservation and screening for combined abiotic and biotic stress resilience resulting from stacked or multifunctional traits. The high presence of salinity tolerance compared with drought stress tolerance, suggests that Vigna taxa are good at developing salt-tolerant traits. Vigna taxa are therefore of high value for legume production in areas that will suffer from salinization under global climate change.
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Affiliation(s)
- Maarten van Zonneveld
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan.
| | - Mohamed Rakha
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan.,Horticulture Department, Faculty of Agriculture, University of Kafrelsheikh, Kafr El-Sheikh, 33516, Egypt
| | - Shin Yee Tan
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan.,Univeristi Malaysia Sabah, Batu 10, 90000, Sandakan, Sabah, Malaysia
| | - Yu-Yu Chou
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan
| | - Ching-Huan Chang
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan
| | - Jo-Yi Yen
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan
| | - Roland Schafleitner
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan
| | - Ramakrishnan Nair
- World Vegetable Center, South Asia, ICRISAT Campus, Patancheru, 502324, Hyderabad, Telangana, India
| | - Ken Naito
- Genetic Resources Center, National Agriculture and Food Science Organization, Tsukuba, Ibaraki, Japan
| | - Svein Ø Solberg
- World Vegetable Center, Headquarters, 60 Yi-Min Liao, Shanhua, Tainan, 74151, Taiwan.,Inland Norway University of Applied Sciences, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, P.O. Box 400, 2418, Elverum, Norway
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25
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Handayani T, Gilani SA, Watanabe KN. Climatic changes and potatoes: How can we cope with the abiotic stresses? BREEDING SCIENCE 2019; 69:545-563. [PMID: 31988619 PMCID: PMC6977456 DOI: 10.1270/jsbbs.19070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/10/2019] [Indexed: 05/06/2023]
Abstract
Climate change triggers increases in temperature, drought, and/or salinity that threaten potato production, because they necessitate specific amounts and quality of water, meanwhile lower temperatures generally support stable crop yields. Various cultivation techniques have been developed to reduce the negative effects of drought, heat and/or salinity stresses on potato. Developing innovative varieties with relevant tolerance to abiotic stress is absolutely necessary to guarantee competitive production under sub-optimal environments. Commercial varieties are sensitive to abiotic stresses, and substantial changes to their higher tolerance levels are not easily achieved because their genetic base is narrow. Nonetheless, there are several other possibilities for genetic enhancement using landraces and wild relatives. The complexity of polysomic genetics and heterozygosity in potato hamper the phenotype evaluation over abiotic stresses and consequent conventional introgression of tolerance traits, which are more challenging than previous successes shown over diseases and insects resistances. Today, potatoes face more challenges with severe abiotic stresses. Potato wild relatives can be explored further using innovative genomic, transcriptomic, proteomic, and metabolomic approaches. At the field level, appropriate cultivation techniques must be applied along with precision farming technology and tolerant varieties developed from various breeding techniques, in order to realize high yield under multiple stresses.
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Affiliation(s)
- Tri Handayani
- Graduate School of Life & Environmental Sciences, University of Tsukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572,
Japan
- Indonesian Vegetable Research Institute,
Jl. Tangkuban Perahu 517, Lembang, West Bandung, West Java, 40391,
Indonesia
| | - Syed Abdullah Gilani
- Department of Biological Sciences and Chemistry, University of Nizwa,
P. O. Box 33, PC 616, Birkat Al Mouz, Nizwa,
Sultanate of Oman
| | - Kazuo N. Watanabe
- Tsukuba-Plant Innovation Research Center, University of Tsukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572,
Japan
- Corresponding author (e-mail: )
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26
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Sharma S, Paul PJ, Kumar CS, Rao PJ, Prashanti L, Muniswamy S, Sharma M. Evaluation and Identification of Promising Introgression Lines Derived From Wild Cajanus Species for Broadening the Genetic Base of Cultivated Pigeonpea [ Cajanus cajan (L.) Millsp.]. FRONTIERS IN PLANT SCIENCE 2019; 10:1269. [PMID: 31695710 PMCID: PMC6817623 DOI: 10.3389/fpls.2019.01269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/11/2019] [Indexed: 05/07/2023]
Abstract
Pigeonpea [Cajanus cajan (L.) Millsp.], a multipurpose and nutritious grain legume crop, is cultivated for its protein-rich seeds mainly in South Asia and Eastern and Southern Africa. In spite of large breeding efforts for pigeonpea improvement in India and elsewhere, genetic enhancement is inadequate largely due to its narrow genetic base and crop susceptibility to stresses. Wild Cajanus species are novel source of genetic variations for the genetic upgradation of pigeonpea cultivars. In the present study, 75 introgression lines (ILs), derived from crosses involving cultivated pigeonpea variety ICPL 87119 and wild Cajanus cajanifolius and Cajanus acutifolius from the secondary gene pool, were evaluated for yield and yield-attributing traits in diverse environments across locations and years. Restricted maximum likelihood (REML) analysis revealed large genetic variations for days to 50% flower, days to maturity, plant height, primary branches per plant, pods per plant, pod weight per plant, 100-seed weight, and grain yield per plant. Superior ILs with mid-early to medium maturity duration identified in this study are useful genetic resources for use in pigeonpea breeding. Additive main effects and multiplicative interaction (AMMI) analysis unfolded large influence of environment and genotype × environment interaction for variations in yield. A few lines such as ICPL 15023 and ICPL 15072 with yield stability were identified, while a number of lines were completely resistant (0%) to sterility mosaic diseases and/or Fusarium wilt. These lines are novel genetic resources for broadening the genetic base of pigeonpea and bring yield stability and stress tolerance. High-yielding lines ICPL 15010, ICPL 15062, and ICPL 15072 have been included in the initial varietal trials (IVTs) of the All India Coordinated Research Project (AICRP) on pigeonpea for wider evaluation across different agro-ecological zones in India for possible release as variety(ies).
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Affiliation(s)
- Shivali Sharma
- Theme Pre-breeding, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pronob J. Paul
- Theme Pre-breeding, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C.V. Sameer Kumar
- Regional Agricultural Research Station, Professor Jayashankar Telangana State Agricultural University, Palem, India
| | - P. Jaganmohan Rao
- Regional Agricultural Research Station, Professor Jayashankar Telangana State Agricultural University, Warangal, India
| | - L. Prashanti
- Regional Agricultural Research Station, Acharya N. G. Ranga Agricultural University, Tirupati, India
| | - S. Muniswamy
- Regional Agricultural Research Station, University of Agricultural Sciences, Kalaburagi, India
| | - Mamta Sharma
- Legume Pathology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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27
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Ojiewo C, Monyo E, Desmae H, Boukar O, Mukankusi‐Mugisha C, Thudi M, Pandey MK, Saxena RK, Gaur PM, Chaturvedi SK, Fikre A, Ganga Rao NPVR, SameerKumar CV, Okori P, Janila P, Rubyogo JC, Godfree C, Akpo E, Omoigui L, Nkalubo S, Fenta B, Binagwa P, Kilango M, Williams M, Mponda O, Okello D, Chichaybelu M, Miningou A, Bationo J, Sako D, Diallo S, Echekwu C, Umar ML, Oteng‐Frimpong R, Mohammed H, Varshney RK. Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers. PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:487-499. [PMID: 31787790 PMCID: PMC6876654 DOI: 10.1111/pbr.12554] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/04/2017] [Indexed: 05/04/2023]
Abstract
Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP-GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large-scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega-initiatives facilitated release of a number of new varieties and also dissemination of on-the-shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics-assisted breeding approaches and rapid generation advancement.
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Affiliation(s)
- Chris Ojiewo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
| | - Emmanuel Monyo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
| | | | - Ousmane Boukar
- International Institute of Tropical Agriculture (IITA)KanoNigeria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stanley Nkalubo
- National Agricultural Research Organization (NARO)NamulongeUganda
| | - Berhanu Fenta
- Ethiopian Institute of Agricultural Research (EIAR)MelkassaEthiopia
| | - Papias Binagwa
- Selian Agricultural Research Institute (SARI)ArushaTanzania
| | | | | | | | - David Okello
- National Semi Arid Resources Research Institute (NaSARRI)SorotiUganda
| | | | - Amos Miningou
- Environmental Institute for Agricultural Research (INERA)OuagadougouBurkina Faso
| | - Joseph Bationo
- Environmental Institute for Agricultural Research (INERA)OuagadougouBurkina Faso
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28
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Rufo R, Alvaro F, Royo C, Soriano JM. From landraces to improved cultivars: Assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers. PLoS One 2019; 14:e0219867. [PMID: 31306459 PMCID: PMC6629082 DOI: 10.1371/journal.pone.0219867] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/02/2019] [Indexed: 11/18/2022] Open
Abstract
Assessment of genetic diversity and population structure in crops is essential for breeding and germplasm conservation. A collection of 354 bread wheat genotypes, including Mediterranean landraces and modern cultivars representative of the ones most widely grown in the Mediterranean Basin, were characterized with 11196 single nucleotide polymorphism (SNP) markers. Total genetic diversity (HT) and polymorphic information content (PIC) were 0.36 and 0.30 respectively for both landraces and modern cultivars. Linkage disequilibrium for the modern cultivars was higher than for the landraces (0.18 and 0.12, respectively). Analysis of the genetic structure showed a clear geographical pattern for the landraces, which were clustered into three subpopulations (SPs) representing the western, northern and eastern Mediterranean, whereas the modern cultivars were structured according to the breeding programmes that developed them: CIMMYT/ICARDA, France/Italy, and Balkan/eastern European countries. The modern cultivars showed higher genetic differentiation (GST) and lower gene flow (0.1673 and 2.49, respectively) than the landraces (0.1198 and 3.67, respectively), indicating a better distinction between subpopulations. The maximum gene flow was observed between landraces from the northern Mediterranean SPs and the modern cultivars released mainly by French and Italian breeding programmes.
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Affiliation(s)
- Rubén Rufo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Fanny Alvaro
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Conxita Royo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
- * E-mail:
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29
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Kumar J, Choudhary AK, Gupta DS, Kumar S. Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses. Int J Mol Sci 2019; 20:E2971. [PMID: 31216660 PMCID: PMC6627977 DOI: 10.3390/ijms20122971] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/18/2019] [Accepted: 05/28/2019] [Indexed: 12/20/2022] Open
Abstract
Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.
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Affiliation(s)
- Jitendra Kumar
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | | | - Debjyoti Sen Gupta
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 6299, Rabat-Institute, Rabat, Morocco.
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30
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Wambugu PW, Ndjiondjop MN, Henry RJ. Role of genomics in promoting the utilization of plant genetic resources in genebanks. Brief Funct Genomics 2019; 17:198-206. [PMID: 29688255 PMCID: PMC5967547 DOI: 10.1093/bfgp/ely014] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Global efforts have seen the world's plant genetic resources (PGRs) conserved in about 1625 germ plasm repositories. Utility of these resources is important in increasing the resilience and productivity of agricultural production systems. However, despite their importance, utility of these resources has been poor. This article reviews the real and potential application of the current advances in genomic technologies in improving the utilization of these resources. The actual and potential application of these genomic approaches in plant identification, phylogenetic analysis, analysing the genetic value of germ plasm, facilitating germ plasm selection in genebanks as well as instilling confidence in international germ plasm exchange system is discussed. We note that if genebanks are to benefit from this genomic revolution, there is need for fundamental changes in the way genebanks are managed, perceived, organized and funded. Increased collaboration between genebank managers and the user community is also recommended.
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Affiliation(s)
- Peterson W Wambugu
- Corresponding author: Robert Henry, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia. Tel.: ±61733460551; Fax: ±61733460555; E-mail:
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31
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Nadeem M, Li J, Yahya M, Wang M, Ali A, Cheng A, Wang X, Ma C. Grain Legumes and Fear of Salt Stress: Focus on Mechanisms and Management Strategies. Int J Mol Sci 2019; 20:E799. [PMID: 30781763 PMCID: PMC6412900 DOI: 10.3390/ijms20040799] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 12/27/2022] Open
Abstract
Salinity is an ever-present major constraint and a major threat to legume crops, particularly in areas with irrigated agriculture. Legumes demonstrate high sensitivity, especially during vegetative and reproductive phases. This review gives an overview of legumes sensitivity to salt stress (SS) and mechanisms to cope with salinity stress under unfavorable conditions. It also focuses on the promising management approaches, i.e., agronomic practices, breeding approaches, and genome editing techniques to improve performance of legumes under SS. Now, the onus is on researchers to comprehend the plants physiological and molecular mechanisms, in addition to various responses as part of their stress tolerance strategy. Due to their ability to fix biological nitrogen, high protein contents, dietary fiber, and essential mineral contents, legumes have become a fascinating group of plants. There is an immense need to develop SS tolerant legume varieties to meet growing demand of protein worldwide. This review covering crucial areas ranging from effects, mechanisms, and management strategies, may elucidate further the ways to develop SS-tolerant varieties and to produce legume crops in unfavorable environments.
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Affiliation(s)
- Muhammad Nadeem
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Jiajia Li
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Muhammad Yahya
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Minghua Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Asif Ali
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Andong Cheng
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Xiaobo Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Chuanxi Ma
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
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32
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Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S. Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1-25. [PMID: 30483819 DOI: 10.1007/s00122-018-3219-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/24/2018] [Indexed: 05/27/2023]
Abstract
CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits. Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross breeding and genome-wide marker-assisted selection followed by selfing. Each line in a CSSL library has a specific marker-defined large donor segment. CSSLs are evaluated for any target phenotype to identify lines significantly different from the parental line. These CSSLs are then used to map quantitative trait loci (QTLs) or causal genes. CSSLs are valuable prebreeding tools for broadening the genetic base of existing cultivars and harnessing the genetic diversity from the wild- and distant-related species. These are resources for genetic map construction, mapping QTLs, genes or gene interactions and their functional analysis for crop improvement. In the last two decades, the utility of CSSLs in identification of novel genomic regions and QTL hot spots influencing a wide range of traits has been well demonstrated in food and commercial crops. This review presents an overview of how CSSLs are developed, their status in major crops and their use in genomic studies and gene discovery.
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Affiliation(s)
- Divya Balakrishnan
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Malathi Surapaneni
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sukumar Mesapogu
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sarla Neelamraju
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India.
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Khera P, Pandey MK, Mallikarjuna N, Sriswathi M, Roorkiwal M, Janila P, Sharma S, Shilpa K, Sudini H, Guo B, Varshney RK. Genetic imprints of domestication for disease resistance, oil quality, and yield component traits in groundnut (Arachis hypogaea L.). Mol Genet Genomics 2018; 294:365-378. [PMID: 30467595 DOI: 10.1007/s00438-018-1511-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 11/08/2018] [Indexed: 11/29/2022]
Abstract
Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful alleles for agronomically important traits. To overcome this genetic barrier, two synthetic tetraploids, viz., ISATGR 1212 (A. duranensis ICG 8123 × A. ipaensis ICG 8206) and ISATGR 265-5A (A. kempff-mercadoi ICG 8164 × A. hoehnei ICG 8190), were used to generate two advanced backcross (AB) populations. The AB-populations, namely, AB-pop1 (ICGV 91114 × ISATGR 1212) and AB-pop2, (ICGV 87846 × ISATGR 265-5A) were genotyped with DArT and SSR markers. Genetic maps were constructed for AB-pop1 and AB-pop2 populations with 258 loci (1415.7 cM map length and map density of 5.5 cM/loci) and 1043 loci (1500.8 cM map length with map density of 1.4 cM/loci), respectively. Genetic analysis identified large number of wild segments in the population and provided a good source of diversity in these populations. Phenotyping of these two populations identified several introgression lines with good agronomic, oil quality, and disease resistance traits. Quantitative trait locus (QTL) analysis showed that the wild genomic segments contributed favourable alleles for foliar disease resistance while cultivated genomic segments mostly contributed favourable alleles for oil quality and yield component traits. These populations, after achieving higher stability, will be useful resource for genetic mapping and QTL discovery for wild species segments in addition to using population progenies in breeding program for diversifying the gene pool of cultivated groundnut.
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Affiliation(s)
- Pawan Khera
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Nalini Mallikarjuna
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manda Sriswathi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Krishna Shilpa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Harikishan Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Baozhu Guo
- Crop Protection and Management Research Unit, US Department of Agriculture-Agricultural Research Service, Tifton, USA
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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Ullah S, Bramley H, Daetwyler H, He S, Mahmood T, Thistlethwaite R, Trethowan R. Genetic Contribution of Emmer Wheat ( Triticum dicoccon Schrank) to Heat Tolerance of Bread Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1529. [PMID: 30524452 PMCID: PMC6257323 DOI: 10.3389/fpls.2018.01529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/28/2018] [Indexed: 05/16/2023]
Abstract
Rising global temperatures cause substantial yield losses in many wheat growing environments. Emmer wheat (Triticum dicoccon Schrank), one of the first wheat species domesticated, carries significant variation for tolerance to abiotic stresses. This study identified new genetic variability for high-temperature tolerance in hexaploid progeny derived from crosses with emmer wheat. Eight hexaploid and 11 tetraploid parents were recombined in 43 backcross combinations using the hexaploid as the recurrent parent. A total of 537 emmer-based hexaploid lines were developed by producing approximately 10 doubled haploids on hexaploid like BC1F1 progeny and subsequent selection for hexaploid morphology. These materials and 17 commercial cultivars and hexaploid recurrent parents were evaluated under two times of sowing in the field, in 2014-2016. The materials were genotyped using a 90K SNP platform and these data were used to estimate the contribution of emmer wheat to the progeny. Significant phenotypic and genetic variation for key agronomical traits including grain yield, TKW and screenings was observed. Many of the emmer derived lines showed improved performance under heat stress (delayed sowing) compared with parents and commercial cultivars. Emmer derived lines were the highest yielding material in both sowing dates. The emmer wheat parent contributed between 1 and 44% of the genome of the derived lines. Emmer derived lines with superior kernel weight and yield generally had a greater genetic contribution from the emmer parent compared to those with lower trait values. The study showed that new genetic variation for key traits such as yield, kernel weight and screenings can be introduced to hexaploid wheat from emmer wheat. These genetic resources should be explored more systematically to stabilize grain yield and quality in a changing climate.
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Affiliation(s)
- Smi Ullah
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
| | - Helen Bramley
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
| | - Hans Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Melbourne, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC, Australia
| | - Sang He
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Melbourne, VIC, Australia
| | - Tariq Mahmood
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Cobbitty, NSW, Australia
| | - Rebecca Thistlethwaite
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
| | - Richard Trethowan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Cobbitty, NSW, Australia
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Molecular Genotyping (SSR) and Agronomic Phenotyping for Utilization of Durum Wheat ( Triticum durum Desf.) Ex Situ Collection from Southern Italy: A Combined Approach Including Pedigreed Varieties. Genes (Basel) 2018; 9:genes9100465. [PMID: 30241387 PMCID: PMC6211131 DOI: 10.3390/genes9100465] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/18/2018] [Accepted: 09/18/2018] [Indexed: 11/17/2022] Open
Abstract
In South Italy durum wheat (Triticum durum Desf.) has a long-time tradition of growing and breeding. Accessions collected and now preserved ex situ are a valuable genetic resource, but their effective use in agriculture and breeding programs remains very low. In this study, a small number (44) of simple sequence repeats (SSR) molecular markers were used to detect pattern of diversity for 136 accessions collected in South Italy over time, to identify the genepool of origin, and establish similarities with 28 Italian varieties with known pedigree grown in Italy over the same time-period. Phenotyping was conducted for 12 morphophysiological characters of agronomic interest. Based on discriminant analysis of principal components (DAPC) and STRUCTURE analysis six groups were identified, the assignment of varieties reflected the genetic basis and breeding strategies involved in their development. Some “old” varieties grown today are the result of evolution through natural hybridization and conservative pure line selection. A small number of molecular markers and little phenotyping coupled with powerful statistical analysis and comparison to pedigreed varieties can provide enough information on the genetic structure of durum wheat germplasm for a quick screening of the germplasm collection able to identify accessions for breeding or introduction in low input agriculture.
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Phenotypic and Physiological Evaluation of Two and Six Rows Barley under Different Environmental Conditions. PLANTS 2018; 7:plants7020039. [PMID: 29734706 PMCID: PMC6027403 DOI: 10.3390/plants7020039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 11/16/2022]
Abstract
In recent years, barley has attracted more interest as a food and feed source because of its high soluble dietary fiber and β-glucan content compared with other small grains. Twenty-five barley genotypes (20 imported genotypes and five check cultivars) were grown in three environments for two successive seasons: 2015/2016 and 2016/2017. The first environment was in El-Nubaria, Alexandria, Egypt during 2015/2016, while the second and third environments were in El-Bostan, Elbhera, Egypt during 2015/2016 and 2016/2017. The experiments were conducted in a randomized complete block design with the three replicates. The primary objectives of the current study were to evaluate the performance of 20 imported barley genotypes under several environmental conditions. The imported materials were superior to the local commercial cultivars for several traits, including grain yield. Therefore, the superior genotypes will be further evaluated and used in barley breeding programs. Our future work will focus on creating several crosses among the selected superior genotypes to improve yield and other important traits, while applying marker-assisted selection.
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Yang K, Nath UK, Biswas MK, Kayum MA, Yi GE, Lee J, Yang TJ, Nou IS. Whole-genome sequencing of Brassica oleracea var. capitata reveals new diversity of the mitogenome. PLoS One 2018; 13:e0194356. [PMID: 29547671 PMCID: PMC5856397 DOI: 10.1371/journal.pone.0194356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 03/01/2018] [Indexed: 11/24/2022] Open
Abstract
Plant mitochondrial genomes (mtDNAs) vary in sequence structure. We assembled the Brassica oleracea var. capitata mtDNA using a mean coverage depth of 25X whole genome sequencing (WGS) and confirmed the presence of eight contigs/fragments by BLASTZ using the previously reported KJ820683 and AP012988 mtDNA as reference. Assembly of the mtDNA sequence reads resulted in a circular structure of 219,975 bp. Our assembled mtDNA, NCBI acc. no. KU831325, contained 34 protein-coding genes, 3 rRNA genes, and 19 tRNA genes with similarity to the KJ820683 and AP012988 reference mtDNA. No large repeats were found in the KU831325 assembly. However, KU831325 showed differences in the arrangement of bases at different regions compared to the previously reported mtDNAs. In the reference mtDNAs KJ820683 and AP012988, contig/fragment number 4 is partitioned into two contigs/fragments, 4a and 4b. However, contig/fragment number 4 was a single contig/fragment with 29,661 bp in KU831325. PCR and qRT-PCR using flanking markers from separate parts of contig/fragment number 4 confirmed it to be a single contig/fragment. In addition, genome re-alignment of the plastid genome and mtDNAs supported the presence of heteroplasmy and reverse arrangement of the heteroplasmic blocks within the other mtDNAs compared to KU831325 that might be one of the causal factors for its diversity. Our results thus confirm the existence of different mtDNAs in diverse B. oleracea subspecies.
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Affiliation(s)
- Kiwoung Yang
- Department of Horticulture, Sunchon National University, Suncheon, Korea
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, Suncheon, Korea
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | - Md Abdul Kayum
- Department of Horticulture, Sunchon National University, Suncheon, Korea
| | - Go-eun Yi
- Department of Horticulture, Sunchon National University, Suncheon, Korea
| | - Jonghoon Lee
- Joeun Seed, Goesan-Gun, Chungcheongbuk-Do, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- * E-mail: (ISN); (TJY)
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, Korea
- * E-mail: (ISN); (TJY)
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Haritha G, Malathi S, Divya B, Swamy BPM, Mangrauthia SK, Sarla N. Oryza nivara Sharma et Shastry. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-71997-9_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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39
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Farooq M, Gogoi N, Hussain M, Barthakur S, Paul S, Bharadwaj N, Migdadi HM, Alghamdi SS, Siddique KHM. Effects, tolerance mechanisms and management of salt stress in grain legumes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 118:199-217. [PMID: 28648997 DOI: 10.1016/j.plaphy.2017.06.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 05/23/2023]
Abstract
Salt stress is an ever-present threat to crop yields, especially in countries with irrigated agriculture. Efforts to improve salt tolerance in crop plants are vital for sustainable crop production on marginal lands to ensure future food supplies. Grain legumes are a fascinating group of plants due to their high grain protein contents and ability to fix biological nitrogen. However, the accumulation of excessive salts in soil and the use of saline groundwater are threatening legume production worldwide. Salt stress disturbs photosynthesis and hormonal regulation and causes nutritional imbalance, specific ion toxicity and osmotic effects in legumes to reduce grain yield and quality. Understanding the responses of grain legumes to salt stress and the associated tolerance mechanisms, as well as assessing management options, may help in the development of strategies to improve the performance of grain legumes under salt stress. In this manuscript, we discuss the effects, tolerance mechanisms and management of salt stress in grain legumes. The principal inferences of the review are: (i) salt stress reduces seed germination (by up to more than 50%) either by inhibiting water uptake and/or the toxic effect of ions in the embryo, (ii) salt stress reduces growth (by more than 70%), mineral uptake, and yield (by 12-100%) due to ion toxicity and reduced photosynthesis, (iii) apoplastic acidification is a good indicator of salt stress tolerance, (iv) tolerance to salt stress in grain legumes may develop through excretion and/or compartmentalization of toxic ions, increased antioxidant capacity, accumulation of compatible osmolytes, and/or hormonal regulation, (v) seed priming and nutrient management may improve salt tolerance in grain legumes, (vi) plant growth promoting rhizobacteria and arbuscular mycorrhizal fungi may help to improve salt tolerance due to better plant nutrient availability, and (vii) the integration of screening, innovative breeding, and the development of transgenics and crop management strategies may enhance salt tolerance and yield in grain legumes on salt-affected soils.
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Affiliation(s)
- Muhammad Farooq
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan; The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, Perth, WA 6001, Australia; College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Nirmali Gogoi
- Department of Environmental Science, Tezpur University, Tezpur 784028, Assam, India
| | - Mubshar Hussain
- Department of Agronomy, Bahauddin Zakariya University Multan, Pakistan
| | - Sharmistha Barthakur
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Sreyashi Paul
- Department of Environmental Science, Tezpur University, Tezpur 784028, Assam, India
| | - Nandita Bharadwaj
- Department of Environmental Science, Tezpur University, Tezpur 784028, Assam, India
| | - Hussein M Migdadi
- College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Salem S Alghamdi
- College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, Perth, WA 6001, Australia
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Dempewolf H, Baute G, Anderson J, Kilian B, Smith C, Guarino L. Past and Future Use of Wild Relatives in Crop Breeding. CROP SCIENCE 2017. [PMID: 0 DOI: 10.2135/cropsci2016.10.0885] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Affiliation(s)
- Hannes Dempewolf
- Global Crop Diversity Trust; Platz der Vereinten Nationen 7 53113 Bonn Germany
- Univ. of British Columbia; Dep. of Botany; 6270 University Blvd. Vancouver BC Canada
| | - Gregory Baute
- Univ. of British Columbia; Dep. of Botany; 6270 University Blvd. Vancouver BC Canada
| | - Justin Anderson
- Univ. of Hawaii at Manoa; Dep. of Tropical Plant & Soil Sciences; 3190 Maile Way Honolulu Hawaii 96822
| | - Benjamin Kilian
- Global Crop Diversity Trust; Platz der Vereinten Nationen 7 53113 Bonn Germany
| | - Chelsea Smith
- Univ. of Waterloo; Dep. of Environment and Resource Studies; 200 University Ave. W. Waterloo ON N2L 3G1 Canada
| | - Luigi Guarino
- Global Crop Diversity Trust; Platz der Vereinten Nationen 7 53113 Bonn Germany
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Expounding the Value of Grain Legumes in the Semi- and Arid Tropics. SUSTAINABILITY 2017. [DOI: 10.3390/su9010060] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Kabbaj H, Sall AT, Al-Abdallat A, Geleta M, Amri A, Filali-Maltouf A, Belkadi B, Ortiz R, Bassi FM. Genetic Diversity within a Global Panel of Durum Wheat (Triticum durum) Landraces and Modern Germplasm Reveals the History of Alleles Exchange. FRONTIERS IN PLANT SCIENCE 2017; 8:1277. [PMID: 28769970 PMCID: PMC5513985 DOI: 10.3389/fpls.2017.01277] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/06/2017] [Indexed: 05/18/2023]
Abstract
Durum wheat is the 10th most important crop in the world, and its use traces back to the origin of agriculture. Unfortunately, in the last century only part of the genetic diversity available for this species has been captured in modern varieties through breeding. Here, the population structure and genetic diversity shared among elites and landraces collected from 32 countries was investigated. A total of 370 entries were genotyped with Axiom 35K array to identify 8,173 segregating single nucleotide polymorphisms (SNPs). Of these, 500 were selected as highly informative with a PIC value above 0.32 and used to test population structure via DAPC, STRUCTURE, and neighbor joining tree. A total of 10 sub-populations could be identified, six constituted by modern germplasm and four by landraces of different geographical origin. Interestingly, genomic comparison among groups indicated that Middle East and Ethiopia had the lowest level of allelic diversity, while breeding programs and landraces collected outside these regions were the richest in rare alleles. Further, phylogenetic analysis among landraces indicated that Ethiopia might represent a second center of origin of durum wheat, rather than a second domestication site as previously believed. Together, the analyses carried here provide a global picture of the available genetic diversity for this crop and shall guide its targeted use by breeders.
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Affiliation(s)
- Hafssa Kabbaj
- International Center for Agricultural Research in the Dry AreasRabat, Morocco
- Department of Plant Science, Mohammed V UniversityRabat, Morocco
| | - Amadou T. Sall
- International Center for Agricultural Research in the Dry AreasRabat, Morocco
- Department of Plant Science, Mohammed V UniversityRabat, Morocco
| | - Ayed Al-Abdallat
- Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan AmmanAmman, Jordan
| | - Mulatu Geleta
- Plant Breeding, Swedish University of Agricultural SciencesAlnarp, Sweden
| | - Ahmed Amri
- International Center for Agricultural Research in the Dry AreasRabat, Morocco
| | | | - Bouchra Belkadi
- Department of Plant Science, Mohammed V UniversityRabat, Morocco
| | - Rodomiro Ortiz
- Plant Breeding, Swedish University of Agricultural SciencesAlnarp, Sweden
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry AreasRabat, Morocco
- *Correspondence: Filippo M. Bassi,
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Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers. PLoS One 2016; 11:e0147213. [PMID: 26808306 PMCID: PMC4726755 DOI: 10.1371/journal.pone.0147213] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/30/2015] [Indexed: 11/21/2022] Open
Abstract
The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8–27.6% and 9.5–23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5–26.5% and 7.5%–15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48–49% and 30.5–45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321–0.854 and 0.299–0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil.
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Dwivedi SL, Ceccarelli S, Blair MW, Upadhyaya HD, Are AK, Ortiz R. Landrace Germplasm for Improving Yield and Abiotic Stress Adaptation. TRENDS IN PLANT SCIENCE 2016; 21:31-42. [PMID: 26559599 DOI: 10.1016/j.tplants.2015.10.012] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/24/2015] [Accepted: 10/15/2015] [Indexed: 05/19/2023]
Abstract
Plant landraces represent heterogeneous, local adaptations of domesticated species, and thereby provide genetic resources that meet current and new challenges for farming in stressful environments. These local ecotypes can show variable phenology and low-to-moderate edible yield, but are often highly nutritious. The main contributions of landraces to plant breeding have been traits for more efficient nutrient uptake and utilization, as well as useful genes for adaptation to stressful environments such as water stress, salinity, and high temperatures. We propose that a systematic landrace evaluation may define patterns of diversity, which will facilitate identifying alleles for enhancing yield and abiotic stress adaptation, thus raising the productivity and stability of staple crops in vulnerable environments.
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Affiliation(s)
- Sangam L Dwivedi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | | | - Matthew W Blair
- Department of Agriculture and Natural Sciences, Lawson Hall, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN, USA
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Ashok K Are
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Department of Plant Breeding, Sundsvagen, 14 Box 101, 23053 Alnarp, Sweden.
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Joshi-Saha A, Reddy KS. Repeat length variation in the 5'UTR of myo-inositol monophosphatase gene is related to phytic acid content and contributes to drought tolerance in chickpea (Cicer arietinum L.). JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5683-90. [PMID: 25888598 DOI: 10.1093/jxb/erv156] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Myo-inositol metabolism plays a significant role in plant growth and development, and is also used as a precursor for many important metabolites, such as ascorbate, pinitol, and phytate. Phytate (inositol hexakisphosphate) is the major storage pool for phosphate in the seeds. It is utilized during seed germination and growth of the developing embryo. In addition, it is implicated in protection against oxidative stress. In the present study, a panel of chickpea accessions was used for an association analysis. Association analysis accounting for population structure and relative kinship identified alleles of a simple sequence repeat marker, NCPGR90, that are associated with both phytic acid content and drought tolerance. These alleles varied with respect to the dinucleotide CT repeats present within the marker. NCPGR90 located to the 5'UTR of chickpea myo-inositol monophosphatase gene (CaIMP) and showed transcript length variation in drought-tolerant and drought-susceptible accessions. CaIMP from a drought-tolerant accession with a smaller repeat was almost 2-fold upregulated as compared to a susceptible accession having a longer repeat, even under control non-stressed conditions. This study suggests an evolution of simple sequence repeat length variation in CaIMP, which might be regulating phytic acid levels to confer drought tolerance in natural populations of chickpea.
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Affiliation(s)
- Archana Joshi-Saha
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Kandali S Reddy
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
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Obidiegwu JE, Bryan GJ, Jones HG, Prashar A. Coping with drought: stress and adaptive responses in potato and perspectives for improvement. FRONTIERS IN PLANT SCIENCE 2015; 6:542. [PMID: 26257752 PMCID: PMC4510777 DOI: 10.3389/fpls.2015.00542] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/03/2015] [Indexed: 05/20/2023]
Abstract
Potato (Solanum tuberosum L.) is often considered as a drought sensitive crop and its sustainable production is threatened due to frequent drought episodes. There has been much research aiming to understand the physiological, biochemical, and genetic basis of drought tolerance in potato as a basis for improving production under drought conditions. The complex phenotypic response of potato plants to drought is conditioned by the interactive effects of the plant's genotypic potential, developmental stage, and environment. Effective crop improvement for drought tolerance will require the pyramiding of many disparate characters, with different combinations being appropriate for different growing environments. An understanding of the interaction between below ground water uptake by the roots and above ground water loss from the shoot system is essential. The development of high throughput precision phenotyping platforms is providing an exciting new tool for precision screening, which, with the incorporation of innovative screening strategies, can aid the selection and pyramiding of drought-related genes appropriate for specific environments. Outcomes from genomics, proteomics, metabolomics, and bioengineering advances will undoubtedly compliment conventional breeding strategies and presents an alternative route toward development of drought tolerant potatoes. This review presents an overview of past research activity, highlighting recent advances with examples from other crops and suggesting future research directions.
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Affiliation(s)
| | - Glenn J. Bryan
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
| | - Hamlyn G. Jones
- Plant Science Division, School of Life Sciences, University of DundeeDundee, UK
- School of Plant Biology, University of Western AustraliaCrawley, WA, Australia
| | - Ankush Prashar
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
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Hema M, Sreenivasulu P, Patil BL, Kumar PL, Reddy DVR. Tropical food legumes: virus diseases of economic importance and their control. Adv Virus Res 2015; 90:431-505. [PMID: 25410108 DOI: 10.1016/b978-0-12-801246-8.00009-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diverse array of food legume crops (Fabaceae: Papilionoideae) have been adopted worldwide for their protein-rich seed. Choice of legumes and their importance vary in different parts of the world. The economically important legumes are severely affected by a range of virus diseases causing significant economic losses due to reduction in grain production, poor quality seed, and costs incurred in phytosanitation and disease control. The majority of the viruses infecting legumes are vectored by insects, and several of them are also seed transmitted, thus assuming importance in the quarantine and in the epidemiology. This review is focused on the economically important viruses of soybean, groundnut, common bean, cowpea, pigeonpea, mungbean, urdbean, chickpea, pea, faba bean, and lentil and begomovirus diseases of three minor tropical food legumes (hyacinth bean, horse gram, and lima bean). Aspects included are geographic distribution, impact on crop growth and yields, virus characteristics, diagnosis of causal viruses, disease epidemiology, and options for control. Effectiveness of selection and planting with virus-free seed, phytosanitation, manipulation of crop cultural and agronomic practices, control of virus vectors and host plant resistance, and potential of transgenic resistance for legume virus disease control are discussed.
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Affiliation(s)
- Masarapu Hema
- Department of Virology, Sri Venkateswara University, Tirupati, India
| | - Pothur Sreenivasulu
- Formerly Professor of Virology, Sri Venkateswara University, Tirupati, India
| | - Basavaprabhu L Patil
- National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi, India
| | - P Lava Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Dodla V R Reddy
- Formerly Principal Virologist, ICRISAT, Patancheru, Hyderabad, India.
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Pazhamala L, Saxena RK, Singh VK, Sameerkumar CV, Kumar V, Sinha P, Patel K, Obala J, Kaoneka SR, Tongoona P, Shimelis HA, Gangarao NVPR, Odeny D, Rathore A, Dharmaraj PS, Yamini KN, Varshney RK. Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan). FRONTIERS IN PLANT SCIENCE 2015; 6:50. [PMID: 25741349 PMCID: PMC4330709 DOI: 10.3389/fpls.2015.00050] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/20/2015] [Indexed: 05/18/2023]
Abstract
Pigeonpea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeonpea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to pigeonpea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the pigeonpea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in pigeonpea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, pigeonpea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeonpea breeding.
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Affiliation(s)
- Lekha Pazhamala
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Vikas K. Singh
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - C. V. Sameerkumar
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Pallavi Sinha
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Kishan Patel
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Jimmy Obala
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | - Seleman R. Kaoneka
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | - P. Tongoona
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | - Hussein A. Shimelis
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | | | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid TropicsNairobi, Kenya
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - P. S. Dharmaraj
- Agricultural Research Station, University of Agricultural SciencesGulbarga, India
| | - K. N. Yamini
- Department of Agricultural Biotechnology, Acharya N. G. Ranga Agricultural UniversityHyderabad, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
- *Correspondence: Rajeev K. Varshney, Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics, Building 300, Patancheru, Hyderabad 502324, India e-mail:
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Sahri A, Chentoufi L, Arbaoui M, Ardisson M, Belqadi L, Birouk A, Roumet P, Muller MH. Towards a comprehensive characterization of durum wheat landraces in Moroccan traditional agrosystems: analysing genetic diversity in the light of geography, farmers' taxonomy and tetraploid wheat domestication history. BMC Evol Biol 2014; 14:264. [PMID: 25528060 PMCID: PMC4300848 DOI: 10.1186/s12862-014-0264-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Crop diversity managed by smallholder farmers in traditional agrosystems is the outcome of historical and current processes interacting at various spatial scales, and influenced by factors such as farming practices and environmental pressures. Only recently have studies started to consider the complexity of these processes instead of simply describing diversity for breeding purposes. A first step in that aim is to add multiple references to the collection of genetic data, including the farmers' varietal taxonomy and practices and the historical background of the crop. RESULTS On the basis of interview data collected in a previous study, we sampled 166 populations of durum wheat varieties in two traditional Moroccan agrosystems, in the Pre-Rif and Atlas Mountains regions. Using a common garden experiment, we detected a high phenotypic variability on traits indicative of taxonomical position and breeding status, namely spike shape and plant height. Populations often combined modern (short) with traditional-like (tall) statures, and classical durum squared spike shape (5 flowers/spikelet) with flat spike shape (3 flowers/ spikelet) representative of primitive domesticated tetraploid wheat (ssp. dicoccum). By contrast, the genetic diversity assessed using 14 microsatellite markers was relatively limited. When compared to the genetic diversity found in a large collection of tetraploid wheat, it corresponded to free-threshing tetraploid wheat. Within Morocco, the two studied regions differed for both genetic diversity and variety names. Within regions, neither geography nor variety names nor even breeding status constituted strong barriers to gene exchange despite a few significant patterns. CONCLUSIONS This first assessment of morphological and genetic diversity allowed pointing out some important factors that may have influenced the structure and evolutionary dynamics of durum wheat in Morocco: the significance of variety names, the occurrence of mixtures within populations, the relative strength of seed exchange between farmers and local adaptation, as well as the fate of modern varieties once they have been introduced. Further, multidisciplinary studies at different spatial scales are needed to better understand these complex agrosystems of invaluable importance for food security.
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Affiliation(s)
- Ali Sahri
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco.
| | - Lamyae Chentoufi
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco.
| | - Mustapha Arbaoui
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco.
| | - Morgane Ardisson
- INRA, UMR 1334, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France.
| | - Loubna Belqadi
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco.
| | - Ahmed Birouk
- Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II, B.P. 6202, Rabat-Instituts, Rabat, Morocco.
| | - Pierre Roumet
- INRA, UMR 1334, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France.
| | - Marie-Hélène Muller
- INRA, UMR 1334, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France.
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