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Diouf M, Zoclanclounon YAB, Mboup PA, Diouf D, Malédon E, Rivallan R, Chair H, Dossa K. Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD. THE PLANT GENOME 2024; 17:e20428. [PMID: 38234122 DOI: 10.1002/tpg2.20428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 12/04/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024]
Abstract
Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome-wide microsatellite marker development across four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono-, di-, and tri-nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at https://y2md.ucad.sn/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam researchers.
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Affiliation(s)
- Moussa Diouf
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | | | - Pape Adama Mboup
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Erick Malédon
- UMR AGAP Institut, CIRAD, Petit Bourg, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Ronan Rivallan
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Hâna Chair
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Komivi Dossa
- UMR AGAP Institut, CIRAD, Petit Bourg, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Agre PA, Clark LV, Garcia-Oliveira AL, Bohar R, Adebola P, Asiedu R, Terauchi R, Asfaw A. Identification of diagnostic KASP-SNP markers for routine breeding activities in yam (Dioscorea spp.). THE PLANT GENOME 2024; 17:e20419. [PMID: 38093501 DOI: 10.1002/tpg2.20419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/16/2023] [Accepted: 11/02/2023] [Indexed: 07/02/2024]
Abstract
Maintaining genetic purity and true-to-type clone identification are important action steps in breeding programs. This study aimed to develop a universal set of kompetitive allele-specific polymerase chain reaction (KASP)-based single nucleotide polymorphism (SNP) markers for routine breeding activities. Ultra-low-density SNP markers were created using an initial set of 173,675 SNPs that were obtained from whole-genome resequencing of 333 diverse white Guinea yam (Dioscorea rotundata Poir) genotypes. From whole-genome resequencing data, 99 putative SNP markers were found and successfully converted to high-throughput KASP genotyping assays. The markers set was validated on 374 genotypes representing six yam species. Out of the 99 markers, 50 were highly polymorphic across the species and could distinguish different yam species and pedigree origins. The selected SNP markers classified the validation population based on the different yam species and identified potential duplicates within yam species. Through penalized analysis, the male parent of progenies involved in polycrosses was successfully predicted and validated. Our research was a trailblazer in validating KASP-based SNP assays for species identification, parental fingerprinting, and quality control (QC) and quality assurance (QA) in yam breeding programs.
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Affiliation(s)
- Paterne A Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Lindsay V Clark
- HPCBio, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ana Luisa Garcia-Oliveira
- Excellence in Breeding (EiB), CIMMYT-ICRAF, UN Av, Nairobi, Kenya
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, Haryana, India
| | - Rajaguru Bohar
- Excellence in Breeding (EiB), CIMMYT-ICRISAT, Hyderabad, Telangana, India
| | - Patrick Adebola
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ryohei Terauchi
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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Asfaw A, Agre P, Matsumoto R, Olatunji AA, Edemodu A, Olusola T, Odom-Kolombia OL, Adesokan M, Alamu OE, Adebola P, Asiedu R, Maziya-Dixon B. Genome-wide dissection of the genetic factors underlying food quality in boiled and pounded white Guinea yam. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4880-4894. [PMID: 37386916 DOI: 10.1002/jsfa.12816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 05/30/2023] [Accepted: 06/30/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND Food quality traits related to the genetics of yam influence the acceptability for its consumption. This study aimed at identifying genetic factors underlying sensory and textural quality attributes of boiled and pounded yam, the two dominant food products from white Guinea yam. RESULTS A genome-wide association study (GWAS) of a panel of 184 genotypes derived from five multi-parent crosses population was conducted. The panel was phenotyped for the qualities of boiled and pounded yam using sensory quality and instrument-based textural profile assays. The genotypes displayed significant variation for most of the attributes. Population differentiation and structure analysis using principal component analysis (PCA) and population structure-based Bayesian information criteria revealed the presence of four well-defined clusters. The GWAS results from a multi-random mixed linear model with kinship and PCA used as covariate identified 13 single-nucleotide polymorphic (SNP) markers significantly associated with the boiled and pounded yam food qualities. The associated SNP markers explained 7.51-13.04% of the total phenotypic variance with a limit of detection exceeding 4. CONCLUSION Regions on chromosomes 7 and 15 were found to be associated with boiled and pounded yam quality attributes from sensory and instrument-based assays. Gene annotation analysis for the regions of associated SNPs revealed co-localization of several known putative genes involved in glucose export, hydrolysis and glycerol metabolism. Our study is one of the first reports of genetic factors underlying the boiled and pounded yam food quality to pave the way for marker-assisted selection in white Guinea yam. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Asrat Asfaw
- Yam Breeding, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Yam Breeding, International Institute of Tropical Agriculture (IITA), Abuja, Nigeria
| | - Paterne Agre
- Yam Breeding, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ryo Matsumoto
- Yam Breeding, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Alex Edemodu
- Yam Breeding, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Theresa Olusola
- Yam Breeding, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Michael Adesokan
- Food and Nutrition Sciences Laboratory, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Oladeji Emmanuel Alamu
- International Institute of Tropical Agriculture, Southern Africa Research and Administration Hub (SARAH) Campus, Lusaka, Zambia
| | - Patrick Adebola
- Yam Breeding, International Institute of Tropical Agriculture (IITA), Abuja, Nigeria
| | - Robert Asiedu
- Yam Breeding, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Busie Maziya-Dixon
- Food and Nutrition Sciences Laboratory, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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Adejumobi II, Agre PA, Adewumi AS, Shonde TE, Cipriano IM, Komoy JL, Adheka JG, Onautshu DO. Association mapping in multiple yam species (Dioscorea spp.) of quantitative trait loci for yield-related traits. BMC PLANT BIOLOGY 2023; 23:357. [PMID: 37434107 DOI: 10.1186/s12870-023-04350-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/16/2023] [Indexed: 07/13/2023]
Abstract
BACKGROUND Yam (Dioscorea spp.) is multiple species with various ploidy level and considered as cash crop in many producing areas. Selection based phenotyping for yield and its related traits such as mosaic virus and anthracnose diseases resistance and plant vigor in multiple species of yam is lengthy however, marker information has proven to enhance selection efficiency. METHODOLOGY In this study, a panel of 182 yam accessions distributed across six yam species were assessed for diversity and marker-traits association study using SNP markers generated from Diversity Array Technology platform. For the traits association analysis, the relation matrix alongside the population structure were used as co-factor to avoid false discovery using Multiple random Mixed Linear Model (MrMLM) followed by gene annotation. RESULTS Accessions performance were significantly different (p < 0.001) across all the traits with high broad-sense heritability (H2). Phenotypic and genotypic correlations showed positive relationships between yield and vigor but negative for yield and yam mosaic disease severity. Population structure revealed k = 6 as optimal clusters-based species. A total of 22 SNP markers were identified to be associated with yield, vigor, mosaic and anthracnose diseases resistance. Gene annotation for the significant SNP loci identified some putative genes associated with primary metabolism, pest and resistance to anthracnose disease, maintenance of NADPH in biosynthetic reaction especially those involving nitro-oxidative stress for resistance to mosaic virus, and seed development, photosynthesis, nutrition use efficiency, stress tolerance, vegetative and reproductive development for tuber yield. CONCLUSION This study provides valuable insights into the genetic control of plant vigor, anthracnose, mosaic virus resistance, and tuber yield in yam and thus, opens an avenue for developing additional genomic resources for markers-assisted selection focusing on multiple yam species.
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Affiliation(s)
- I I Adejumobi
- Department of Biotechnology, Faculty of Science, University of Kisangani, Kisangani, DR, Congo
- International Institute of Tropical Agriculture, Lagos, Nigeria
| | - Paterne A Agre
- International Institute of Tropical Agriculture, Lagos, Nigeria.
| | - A S Adewumi
- International Institute of Tropical Agriculture, Lagos, Nigeria
| | - T E Shonde
- International Institute of Tropical Agriculture, Lagos, Nigeria
| | - I M Cipriano
- Department of Biotechnology, Faculty of Science, University of Kisangani, Kisangani, DR, Congo
| | - J L Komoy
- Department of Biotechnology, Faculty of Science, University of Kisangani, Kisangani, DR, Congo
| | - J G Adheka
- Department of Biotechnology, Faculty of Science, University of Kisangani, Kisangani, DR, Congo
| | - D O Onautshu
- Department of Biotechnology, Faculty of Science, University of Kisangani, Kisangani, DR, Congo
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Chang Y, Sun H, Liu S, He Y, Zhao S, Wang J, Wang T, Zhang J, Gao J, Yang Q, Li M, Zhao X. Identification of BBX gene family and its function in the regulation of microtuber formation in yam. BMC Genomics 2023; 24:354. [PMID: 37365511 DOI: 10.1186/s12864-023-09406-1] [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: 01/18/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023] Open
Abstract
BBX proteins play important roles in all of the major light-regulated developmental processes. However, no systematic analysis of BBX gene family regarding the regulation of photoperiodic microtuber formation has been previously performed in yam. In this study, a systematic analysis on the BBX gene family was conducted in three yam species, with the results, indicating that this gene plays a role in regulating photoperiodic microtuber formation. These analyses included identification the BBX gene family in three yam species, their evolutionary relationships, conserved domains, motifs, gene structure, cis-acting elements, and expressional patterns. Based on these analyses, DoBBX2/DoCOL5 and DoBBX8/DoCOL8 showing the most opposite pattern of expression during microtuber formation were selected as candidate genes for further investigation. Gene expression analysis showed DoBBX2/DoCOL5 and DoBBX8/DoCOL8 were highest expressed in leaves and exhibited photoperiod responsive expression patterns. Besides, the overexpression of DoBBX2/DoCOL5 and DoBBX8/DoCOL8 in potato accelerated tuber formation under short-day (SD) conditions, whereas only the overexpression of DoBBX8/DoCOL8 enhanced the accelerating effect of dark conditions on tuber induction. Tuber number was increased in DoBBX8/DoCOL8 overexpressing plants under dark, as well as in DoBBX2/DoCOL5 overexpressing plants under SD. Overall, the data generated in this study may form the basis of future functional characterizations of BBX genes in yam, especially regarding their regulation of microtuber formation via the photoperiodic response pathway.
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Affiliation(s)
- Yingying Chang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Haoyuan Sun
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shiyu Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yulong He
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shanshan Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Jiage Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Tianle Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
- Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province / Engineering Laboratory of Green Medicinal Material Biotechnology of Henan Province, Xinxiang, 453007, China
| | - Jiangli Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
- Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province / Engineering Laboratory of Green Medicinal Material Biotechnology of Henan Province, Xinxiang, 453007, China
| | - Jin Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Xinxiang, 453007, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Xinxiang, 453007, China
| | - Mingjun Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
- Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province / Engineering Laboratory of Green Medicinal Material Biotechnology of Henan Province, Xinxiang, 453007, China.
| | - Xiting Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
- Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province / Engineering Laboratory of Green Medicinal Material Biotechnology of Henan Province, Xinxiang, 453007, China.
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Dwivedi SL, Chapman MA, Abberton MT, Akpojotor UL, Ortiz R. Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses. Front Genet 2023; 14:1193780. [PMID: 37396035 PMCID: PMC10311922 DOI: 10.3389/fgene.2023.1193780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.
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Affiliation(s)
| | - Mark A. Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Xiao Y, Wang S, Ali A, Shan N, Luo S, Sun J, Zhang H, Xie G, Shen S, Huang Y, Zhou Q. Cultivation pattern affects starch structure and physicochemical properties of yam (Dioscorea persimilis). Int J Biol Macromol 2023; 242:125004. [PMID: 37217061 DOI: 10.1016/j.ijbiomac.2023.125004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/21/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
Yam (Dioscorea spp.) is a major food source in many countries due to its tuber rich in starch (60 %-89 % of the dry weight) and various important micronutrients. Orientation Supergene Cultivation (OSC) pattern is a simple and efficient cultivation mode developed in China in recent years. However, little is known about its effect on yam tuber starch. In this study, the starchy tuber yield, starch structure and physicochemical properties were compared and analyzed in detail between OSC and Traditional Vertical Cultivation (TVC) with Dioscorea persimilis "zhugaoshu", a widely cultivated variety. The results proved that OSC significantly increased tuber yield (23.76 %-31.86 %) and commodity quality (more smooth skin) compared with TVC in three consecutive years of field experiments. Moreover, OSC increased amylopectin content, resistant starch content, granule average diameter and average degree of crystallinity by 2.7 %, 5.8 %, 14.7 % and 9.5 %, respectively, while OSC decreased starch molecular weight (Mw). These traits resulted in starch with lower thermal properties (To, Tp, Tc, ΔHgel), but higher pasting properties (PV, TV). Our results indicated that cultivation pattern affected the yam production and starch physicochemical properties. It would not only provide a practical basis for OSC promotion, but also provide valuable information on how to guide the yam starch end use in food and non-food industries.
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Affiliation(s)
- Yao Xiao
- Jiangxi Province Key Laboratory of Root and Tuber Crops Biology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shenglin Wang
- Jiangxi Province Key Laboratory of Root and Tuber Crops Biology, Jiangxi Agricultural University, Nanchang 330045, China; Queensland Department of Agriculture and Fisheries, PO Box 1054, Mareeba, QLD 4880, Australia
| | - Asjad Ali
- Queensland Department of Agriculture and Fisheries, PO Box 1054, Mareeba, QLD 4880, Australia
| | - Nan Shan
- Jiangxi Province Key Laboratory of Root and Tuber Crops Biology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Sha Luo
- Jiangxi Province Key Laboratory of Root and Tuber Crops Biology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jingyu Sun
- Jiangxi Province Key Laboratory of Root and Tuber Crops Biology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hongyu Zhang
- Jiangxi Province Key Laboratory of Root and Tuber Crops Biology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Guoqiang Xie
- Jiujiang Academy of Agricultural Sciences, Jiujiang 332000, China
| | - Shaohua Shen
- Jiujiang Academy of Agricultural Sciences, Jiujiang 332000, China
| | - Yingjin Huang
- Jiangxi Province Key Laboratory of Root and Tuber Crops Biology, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Qinghong Zhou
- Jiangxi Province Key Laboratory of Root and Tuber Crops Biology, Jiangxi Agricultural University, Nanchang 330045, China.
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Baffour-Ata F, Awugyi M, Ofori NS, Hayfron EN, Amekudzi CE, Ghansah A, Akorli R. Determinants of yam farmers' adaptation practices to climate variability in the Ejura Sekyedumase municipality, Ghana. Heliyon 2023; 9:e14090. [PMID: 36923859 PMCID: PMC10008982 DOI: 10.1016/j.heliyon.2023.e14090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
This study assessed the factors affecting yam farmers' adaptation practices to climate variability in the Ejura Sekyedumase Municipality, Ghana. Primary data was collected through 160 household surveys and 8 key informant interviews. Binary logistic regression was used to assess the factors affecting the yam farmers' choice of adaptation practices. Findings revealed that the yam farmers perceived climate variability through changes in the onset and patterns of rainfall, increasing windstorms, and rising temperatures. The yam farmers perceived the adverse effects of climate variability on their yam production to include a reduction in yam yields (98%), decreased income of farmers (97%), and reduced soil fertility (97%). Findings also showed that the yam farmers utilized key adaptation practices including changing the planting period of yam (88%), planting early-maturing yam seeds/varieties (86%), and intercropping yam with other crops (84%). The key adaptation practices implemented by the farmers were significantly affected by socioeconomic factors including age, years of stay in the community, household size, access to extension services, marital status, education, farming experience, access to climate information, estimated farm size, and estimated farm income (p < 0.05). The empirical findings of this study reinforce the importance of policymakers devising suitable climate variability adaptation policies for yam farmers in Ghana while taking into cognizance the socioeconomic factors that could affect their adoption of such adaptation practices.
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Affiliation(s)
- Frank Baffour-Ata
- Department of Environmental Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Margaret Awugyi
- Department of Environmental Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Norberta Sitsofe Ofori
- Department of Environmental Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Efua Nyansema Hayfron
- Department of Environmental Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Christian Elorm Amekudzi
- Department of Environmental Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Anita Ghansah
- Department of Environmental Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ruth Akorli
- Department of Environmental Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Agre PA, Edemodu A, Obidiegwu JE, Adebola P, Asiedu R, Asfaw A. Variability and genetic merits of white Guinea yam landraces in Nigeria. FRONTIERS IN PLANT SCIENCE 2023; 14:1051840. [PMID: 36814760 PMCID: PMC9940711 DOI: 10.3389/fpls.2023.1051840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Landraces represent a significant gene pool of African cultivated white Guinea yam diversity. They could, therefore, serve as a potential donor of important traits such as resilience to stresses as well as food quality attributes that may be useful in modern yam breeding. This study assessed the pattern of genetic variability, quantitative trait loci (QTLs), alleles, and genetic merits of landraces, which could be exploited in breeding for more sustainable yam production in Africa. METHODS A total of 86 white Guinea yam landraces representing the popular landraces in Nigeria alongside 16 elite clones were used for this study. The yam landraces were genotyped using 4,819 DArTseq SNP markers and profiled using key productivity and food quality traits. RESULTS AND DISCUSSION Genetic population structure through admixture and hierarchical clustering methods revealed the presence of three major genetic groups. Genome-wide association scan identified thirteen SNP markers associated with five key traits, suggesting that landraces constitute a source of valuable genes for productivity and food quality traits. Further dissection of their genetic merits in yam breeding using the Genomic Prediction of Cross Performance (GPCP) allowed identifying several landraces with high crossing merit for multiple traits. Thirteen landraces were identified as potential genitors to develop segregating progenies to improve multiple traits simultaneously for desired gains in yam breeding. Results of this study provide valuable insights into the patterns and the merits of local genetic diversity which can be utilized for identifying desirable genes and alleles of interest in yam breeding for Africa.
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Affiliation(s)
- Paterne A. Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Alex Edemodu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Jude E. Obidiegwu
- National Root Crops Research Institute, Umudike, Abia State, Nigeria
| | - Patrick Adebola
- International Institute of Tropical Agriculture (IITA), Abuja, Nigeria
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Abuja, Nigeria
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Natsume S, Sugihara Y, Kudoh A, Oikawa K, Shimizu M, Ishikawa Y, Nishihara M, Abe A, Innan H, Terauchi R. Genome Analysis Revives a Forgotten Hybrid Crop Edo-dokoro in the Genus Dioscorea. PLANT & CELL PHYSIOLOGY 2022; 63:1667-1678. [PMID: 35876055 PMCID: PMC9680860 DOI: 10.1093/pcp/pcac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/17/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
A rhizomatous Dioscorea crop 'Edo-dokoro' was described in old records of Japan, but its botanical identity has not been characterized. We found that Edo-dokoro is still produced by four farmers in Tohoku-machi of the Aomori prefecture, Japan. The rhizomes of Edo-dokoro are a delicacy to the local people and are sold in the markets. Morphological characters of Edo-dokoro suggest its hybrid origin between the two species, Dioscorea tokoro and Dioscorea tenuipes. Genome analysis revealed that Edo-dokoro likely originated by hybridization of a male D. tokoro to a female D. tenuipes, followed by a backcross with a male plant of D. tokoro. Edo-dokoro is a typical minor crop possibly maintained for more than 300 years but now almost forgotten by the public. We hypothesize that there are many such uncharacterized genetic heritages passed over generations by small-scale farmers that await serious scientific investigation for future use and improvement by using modern genomics information.
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Affiliation(s)
- Satoshi Natsume
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Yu Sugihara
- Crop Evolution Laboratory, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
| | - Aoi Kudoh
- Crop Evolution Laboratory, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
| | - Kaori Oikawa
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Yuko Ishikawa
- Crop Evolution Laboratory, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
| | | | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Hideki Innan
- Laboratory of Population Genetics and Genome Evolution, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
- Crop Evolution Laboratory, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
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11
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Akagi T, Jung K, Masuda K, Shimizu KK. Polyploidy before and after domestication of crop species. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102255. [PMID: 35870416 DOI: 10.1016/j.pbi.2022.102255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/01/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems. This review also clarifies the molecular basis of some agriculturally advantageous traits of polyploid crops, including yield increments in polyploid cotton via subfunctionalization, modification of a separated sexuality to selfing in polyploid persimmon via neofunctionalization, and transition to a selfing system via nonfunctionalization combined with epistatic interaction between duplicated S-loci. The rapid progress in genomics and genetics is discussed along with how this will facilitate functional studies of understudied polyploid crop species.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
| | - Katharina Jung
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland
| | - Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, 244-0813 Totsuka-ward, Yokohama, Japan.
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12
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Asfaw A, Mondo JM, Agre PA, Asiedu R, Akoroda MO. Association mapping of plant sex and cross-compatibility related traits in white Guinea yam (Dioscorea rotundata Poir.) clones. BMC PLANT BIOLOGY 2022; 22:294. [PMID: 35705900 PMCID: PMC9199169 DOI: 10.1186/s12870-022-03673-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND White Guinea yam (Dioscorea rotundata) is primarily a dioecious species with distinct male and female plants. Its breeding is constrained by sexual reproduction abnormalities, resulting in low success rates in cross-pollination. An accurate method for early detection of this plant's sex and compatible fertile parents at the seedling stage would improve levels of cross-pollination success in breeding. We used the genome-wide association studies (GWAS) to dissect the molecular basis of plant sex and cross-compatibility-related traits in a panel of 112 parental clones used in D. rotundata crossing blocks from 2010 to 2020. RESULTS Population structure and phylogeny analyses using 8326 single nucleotide polymorphism (SNP) markers grouped the 112 white yam clones into three subpopulations. Using Multi-locus random-SNP-effect Mixed Linear Model, we identified three, one, and three SNP markers that were significantly associated with the average crossability rate (ACR), the percentage of high crossability (PHC), and the plant sex, respectively. In addition, five genes considered to be directly linked to sexual reproduction or regulating the balance of sex hormones were annotated from chromosomal regions controlling the assessed traits. This study confirmed the female heterogametic sex determination (ZZ/ZW) system proposed for D. rotundata. CONCLUSIONS This study provides valuable insights on the genomic control of sex identity and cross-pollination success in D. rotundata. It, therefore, opens an avenue for developing molecular markers for predicting plant sex and cross-pollination success at the early growth stage before field sex expression in this crop.
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Affiliation(s)
- Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Ibadan, 5320, Nigeria
| | - Jean M Mondo
- International Institute of Tropical Agriculture (IITA), Ibadan, 5320, Nigeria
- Institute of Life and Earth Sciences, Pan African University, University of Ibadan, Ibadan, 200284, Nigeria
- Department of Crop Production, Université Evangélique en Afrique (UEA), Bukavu, 3323, Democratic Republic of Congo
| | - Paterne A Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, 5320, Nigeria.
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan, 5320, Nigeria
| | - Malachy O Akoroda
- Department of Agronomy, University of Ibadan, Ibadan, 200284, Nigeria
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13
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Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. THE NEW PHYTOLOGIST 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
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Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
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14
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Bredeson JV, Lyons JB, Oniyinde IO, Okereke NR, Kolade O, Nnabue I, Nwadili CO, Hřibová E, Parker M, Nwogha J, Shu S, Carlson J, Kariba R, Muthemba S, Knop K, Barton GJ, Sherwood AV, Lopez-Montes A, Asiedu R, Jamnadass R, Muchugi A, Goodstein D, Egesi CN, Featherston J, Asfaw A, Simpson GG, Doležel J, Hendre PS, Van Deynze A, Kumar PL, Obidiegwu JE, Bhattacharjee R, Rokhsar DS. Chromosome evolution and the genetic basis of agronomically important traits in greater yam. Nat Commun 2022; 13:2001. [PMID: 35422045 PMCID: PMC9010478 DOI: 10.1038/s41467-022-29114-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/08/2022] [Indexed: 12/14/2022] Open
Abstract
The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Ibukun O Oniyinde
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Nneka R Okereke
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - Olufisayo Kolade
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Ikenna Nnabue
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | | | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900, Olomouc, Czech Republic
| | - Matthew Parker
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Jeremiah Nwogha
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | | | | | - Robert Kariba
- World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- African Orphan Crops Consortium, Nairobi, Kenya
| | - Samuel Muthemba
- World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- African Orphan Crops Consortium, Nairobi, Kenya
| | - Katarzyna Knop
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Anna V Sherwood
- School of Life Sciences, University of Dundee, Dundee, UK
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Antonio Lopez-Montes
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
- International Trade Center, Accra, Ghana
| | - Robert Asiedu
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Ramni Jamnadass
- World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- African Orphan Crops Consortium, Nairobi, Kenya
| | - Alice Muchugi
- World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- African Orphan Crops Consortium, Nairobi, Kenya
| | | | - Chiedozie N Egesi
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- Cornell University, Ithaca, NY, 14850, USA
| | | | - Asrat Asfaw
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Gordon G Simpson
- School of Life Sciences, University of Dundee, Dundee, UK
- James Hutton Institute, Dundee, UK
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900, Olomouc, Czech Republic
| | - Prasad S Hendre
- World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- African Orphan Crops Consortium, Nairobi, Kenya
| | | | - Pullikanti Lava Kumar
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Jude E Obidiegwu
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria.
| | - Ranjana Bhattacharjee
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria.
| | - Daniel S Rokhsar
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- DOE Joint Genome Institute, Berkeley, CA, USA.
- Okinawa Institute of Science and Technology, Onna, Okinawa, Japan.
- Chan-Zuckerberg BioHub, 499 Illinois St., San Francisco, CA, 94158, USA.
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15
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How 'omics technologies can drive plant engineering, ecosystem surveillance, human and animal health. Emerg Top Life Sci 2022; 6:137-139. [PMID: 35403675 PMCID: PMC9278818 DOI: 10.1042/etls20220020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 11/17/2022]
Abstract
'Omics describes a broad collection of research tools and techniques that enable researchers to collect data about biological systems at a very large, or near-complete, scale. These include sequencing of individual and community genomes (genomics, metagenomics), characterization and quantification of gene expression (transcriptomics), metabolite abundance (metabolomics), protein content (proteomics) and phosphorylation (phospho-proteomics), amongst many others. Though initially exploited as tools for fundamental discovery, 'omics techniques are now used extensively in applied and translational research, for example in plant and animal breeding, biomarker development and drug discovery. In this collection of reviews, we aimed to introduce readers to current and future applications of 'omics technologies to solve real-world problems.
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17
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Kumar A, Anju T, Kumar S, Chhapekar SS, Sreedharan S, Singh S, Choi SR, Ramchiary N, Lim YP. Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security. Int J Mol Sci 2021; 22:8093. [PMID: 34360856 PMCID: PMC8348985 DOI: 10.3390/ijms22158093] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022] Open
Abstract
Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. Traditional food plants are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in situations such as COVID-19 and in times of other pandemics. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realizing the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of TFPs for their improvements, cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in several TFPs. This suggests that there is ample scope for improvement of TFPs for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.
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Affiliation(s)
- Ajay Kumar
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Thattantavide Anju
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Sushil Kumar
- Department of Botany, Govt. Degree College, Kishtwar 182204, Jammu and Kashmir, India;
| | - Sushil Satish Chhapekar
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Sajana Sreedharan
- Department of Plant Science, Central University of Kerala, Kasaragod 671316, Kerala, India; (T.A.); (S.S.)
| | - Sonam Singh
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Su Ryun Choi
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, Delhi, India
| | - Yong Pyo Lim
- Molecular Genetics & Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea; (S.S.C.); (S.S.); (S.R.C.)
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18
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Carey S, Yu Q, Harkess A. The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing. Genes (Basel) 2021; 12:381. [PMID: 33800038 PMCID: PMC8000587 DOI: 10.3390/genes12030381] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/21/2023] Open
Abstract
For centuries, scientists have been intrigued by the origin of dioecy in plants, characterizing sex-specific development, uncovering cytological differences between the sexes, and developing theoretical models. Through the invention and continued improvements in genomic technologies, we have truly begun to unlock the genetic basis of dioecy in many species. Here we broadly review the advances in research on dioecy and sex chromosomes. We start by first discussing the early works that built the foundation for current studies and the advances in genome sequencing that have facilitated more-recent findings. We next discuss the analyses of sex chromosomes and sex-determination genes uncovered by genome sequencing. We synthesize these results to find some patterns are emerging, such as the role of duplications, the involvement of hormones in sex-determination, and support for the two-locus model for the origin of dioecy. Though across systems, there are also many novel insights into how sex chromosomes evolve, including different sex-determining genes and routes to suppressed recombination. We propose the future of research in plant sex chromosomes should involve interdisciplinary approaches, combining cutting-edge technologies with the classics to unravel the patterns that can be found across the hundreds of independent origins.
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Affiliation(s)
- Sarah Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX 75252, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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