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Budi T, Kumnan N, Singchat W, Chalermwong P, Thong T, Wongloet W, Faniriharisoa Maxime Toky R, Pathomvanich P, Panthum T, Wattanadilokchatkun P, Farhan Ahmad S, Tanglertpaibul N, Vangnai K, Chaiyes A, Yokthongwattana C, Sinthuvanich C, Han K, Muangmai N, Koga A, Nunome M, Sawatdichaikul O, Duengkae P, Matsuda Y, Srikulnath K. Weak purifying selection in allelic diversity of the ADSL gene in indigenous and local chicken breeds and red junglefowl in Thailand. Gene 2024; 923:148587. [PMID: 38768877 DOI: 10.1016/j.gene.2024.148587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
Abstract
High levels of purine and uric acid, which are associated with health issues such as gout and cardiovascular disease, are found in the meat of fast-growing broiler chickens, which raises concerns about the quality of chicken meat and the health of the consumers who consume it. High genetic homogeneity and uniformity, particularly in genes involved in the synthesis of inosine monophosphate (IMP) and subsequent process of purine synthesis, which are associated with the meat quality, are exhibited in commercial broiler chickens owing to intensive inbreeding programs. Adenosine succinate lyase (ADSL) is a key enzyme involved in de novo purine biosynthetic pathway and its genetic polymorphisms affect IMP metabolism and purine content. In this study, we investigated the polymorphism of the ADSL gene in indigenous and local chicken breeds and red junglefowl in Thailand, using metabarcoding and genetic diversity analyses. Five alleles with 73 single nucleotide polymorphisms in exon 2, including missense and silent mutations, which may act on the synthesis efficiency of IMP and purine. Their protein structures revealed changes in amino acid composition that may affect ADSL enzyme activity. Weak purifying selection in these ADSL alleles was observed in the chicken population studied, implying that the variants have minor fitness impacts and a greater probability of fixation of beneficial mutations than strong purifying selection. A potential selective sweep was observed in Mae Hong Son chickens, whose purine content was lower than that in other breeds. This suggests a potential correlation between variations of the ADSL gene and reduced purine content and an impact of ADSL expression on the quality of chicken meat. However, further studies are required to validate its potential availability as a genetic marker for selecting useful traits that are beneficial to human health and well-being.
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Affiliation(s)
- Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nichakorn Kumnan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Rajaonarison Faniriharisoa Maxime Toky
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Prangyapawn Pathomvanich
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nivit Tanglertpaibul
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kanithaporn Vangnai
- Department of Food Science and Technology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Aingorn Chaiyes
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi 11120, Thailand
| | - Chotika Yokthongwattana
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Chomdao Sinthuvanich
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea; Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Republic of Korea
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Mitsuo Nunome
- Department of Zoology, Faculty of Science, Okayama University of Science, Ridai-cho 1-1, Kita-ku, Okayama City, Okayama 700-0005, Japan
| | - Orathai Sawatdichaikul
- Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Yoichi Matsuda
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
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Malik G, Jabeen A, Mir JI, Shah RA, Shah MA, Dinkar V, Sheikh MA, Kumar R, Sharma OC, Verma MK. Genetic diversity, population structure and marker-trait associations in Indian kale ( Brassica oleracea L. gp. acephala) using cross-species microsatellite markers. Heliyon 2024; 10:e29521. [PMID: 38681616 PMCID: PMC11046235 DOI: 10.1016/j.heliyon.2024.e29521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024] Open
Abstract
Kale is known for its exceptional nourishing and functional benefits to human body. However, it is an understudied species from genomic as well as agronomic aspects. It is important to characterize niche kale germplasms around the world to systematically conserve and utilize its genetic variability, especially for commercial traits in the interest of growers, consumers and industry. With this view, genomic and phenotypic characterizations of 62 Kashmiri kale accessions including popular landraces were done to estimate and partition genetic diversity, understand trait relationships, develop population structure and divulge marker-trait associations of economic significance. Sixty-six cross species microsatellite (SSR) markers within Brassica genus amplified 269 alleles in the germplasm. Their polymorphic information content (PIC) ranged from 0.00078 to 0.953 with an average of 0.407. The population structure analysis and neighbour joining tree clustering categorized the germplasm into three sub-populations. AMOVA revealed more within-population variance (67.73 %) than among-populations (32.27 %) variance. The principal component analysis (PCA) involving 24 agronomical traits revealed seven PCs (PC1 to PC7) having Eigen values more than 1, which explained a cumulative variation of 69.21 %. Association mapping with respect to these 24 agronomical traits using mixed linear model and general linear model revealed six overlapping significant marker-trait relationships with five being significant at probability value of 0.001/0.0001. The highly significant associations of two SSRs with economically important traits (siliqua length and seed weight) significantly correlated/related with leaf yield and seed yield were revealed for their possible utilization in marker assisted breeding for higher leaf and seed yields.
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Affiliation(s)
- Geetika Malik
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Asma Jabeen
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Javid Iqbal Mir
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Rafiq Ahmad Shah
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Mohd Abas Shah
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Vishal Dinkar
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Muneer Ahmad Sheikh
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Ravinder Kumar
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Om Chand Sharma
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
| | - Mahendra Kumar Verma
- Indian Council of Agricultural Research-Central Institute of Temperate Horticulture, Srinagar, Jammu & Kashmir, India, 191132
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Panthum T, Ariyaraphong N, Wongloet W, Wattanadilokchatkun P, Laopichienpong N, Rasoarahona R, Singchat W, Ahmad SF, Kraichak E, Muangmai N, Duengkae P, Fukuda Y, Banks S, Temsiripong Y, Ezaz T, Srikulnath K. Preserving Pure Siamese Crocodile Populations: A Comprehensive Approach Using Multi-Genetic Tools. BIOLOGY 2023; 12:1428. [PMID: 37998027 PMCID: PMC10669835 DOI: 10.3390/biology12111428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/04/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite and mitochondrial DNA data to establish the criteria for identifying species and their hybrids; however, the results may have been influenced by biased allelic frequencies and genetic drift within the examined population. To overcome these limitations and identify the true signals of selection, alternative DNA markers and a diverse set of populations should be employed. Therefore, this study used DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm the genetic scenario of the parental species and their hybrids. A population of saltwater crocodiles from Australia was used to compare the distribution of species-diagnostic SNPs. Different analytical approaches were compared to diagnose the level of hybridization when an admixture was present, wherein three individuals had potential backcrossing. Approximately 17.00-26.00% of loci were conserved between the Siamese and saltwater crocodile genomes. Species-diagnostic SNP loci for Siamese and saltwater crocodiles were identified as 8051 loci and 1288 loci, respectively. To validate the species-diagnostic SNP loci, a PCR-based approach was used by selecting 20 SNP loci for PCR primer design, among which 3 loci were successfully able to differentiate the actual species and different hybridization levels. Mitochondrial and nuclear genetic information, including microsatellite genotyping and species-diagnostic DNA markers, were combined as a novel method that can compensate for the limitations of each method. This method enables conservation prioritization before release into the wild, thereby ensuring sustainable genetic integrity for long-term species survival through reintroduction and management programs.
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Affiliation(s)
- Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nattakan Ariyaraphong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nararat Laopichienpong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
| | - Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Department of Botany, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Yusuke Fukuda
- Department of Environment, Parks and Water Security, Northern Territory Government, Darwin, NT 0830, Australia;
| | - Sam Banks
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, NT 0909, Australia;
| | | | - Tariq Ezaz
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Bruce, ACT 2617, Australia;
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
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Rasoarahona R, Wattanadilokchatkun P, Panthum T, Thong T, Singchat W, Ahmad SF, Chaiyes A, Han K, Kraichak E, Muangmai N, Koga A, Duengkae P, Antunes A, Srikulnath K. Optimizing Microsatellite Marker Panels for Genetic Diversity and Population Genetic Studies: An Ant Colony Algorithm Approach with Polymorphic Information Content. BIOLOGY 2023; 12:1280. [PMID: 37886990 PMCID: PMC10604496 DOI: 10.3390/biology12101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/28/2023]
Abstract
Microsatellites are polymorphic and cost-effective. Optimizing reduced microsatellite panels using heuristic algorithms eases budget constraints in genetic diversity and population genetic assessments. Microsatellite marker efficiency is strongly associated with its polymorphism and is quantified as the polymorphic information content (PIC). Nevertheless, marker selection cannot rely solely on PIC. In this study, the ant colony optimization (ACO) algorithm, a widely recognized optimization method, was adopted to create an enhanced selection scheme for refining microsatellite marker panels, called the PIC-ACO selection scheme. The algorithm was fine-tuned and validated using extensive datasets of chicken (Gallus gallus) and Chinese gorals (Naemorhedus griseus) from our previous studies. In contrast to basic optimization algorithms that stochastically initialize potential outputs, our selection algorithm utilizes the PIC values of markers to prime the ACO process. This increases the global solution discovery speed while reducing the likelihood of becoming trapped in local solutions. This process facilitated the acquisition of a cost-efficient and optimized microsatellite marker panel for studying genetic diversity and population genetic datasets. The established microsatellite efficiency metrics such as PIC, allele richness, and heterozygosity were correlated with the actual effectiveness of the microsatellite marker panel. This approach could substantially reduce budgetary barriers to population genetic assessments, breeding, and conservation programs.
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Affiliation(s)
- Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Aingorn Chaiyes
- School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Pakkret Nonthaburi 11120, Thailand;
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Republic of Korea
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Agostinho Antunes
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University, Bangkok 10900, Thailand
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5
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Wongloet W, Singchat W, Chaiyes A, Ali H, Piangporntip S, Ariyaraphong N, Budi T, Thienpreecha W, Wannakan W, Mungmee A, Jaisamut K, Thong T, Panthum T, Ahmad SF, Lisachov A, Suksavate W, Muangmai N, Chuenka R, Nunome M, Chamchumroon W, Han K, Nuangmek A, Matsuda Y, Duengkae P, Srikulnath K. Environmental and Socio-Cultural Factors Impacting the Unique Gene Pool Pattern of Mae Hong-Son Chicken. Animals (Basel) 2023; 13:1949. [PMID: 37370459 PMCID: PMC10295432 DOI: 10.3390/ani13121949] [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: 03/03/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Understanding the genetic diversity of domestic chicken breeds under the impact of socio-cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son Province, Thailand; however, its genetic characterization, origin, and diversity remain poorly understood. Here, we studied the socio-cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed and investigated its diversity and allelic gene pool. We genotyped 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data to evaluate genetic diversity and assessed spatial habitat suitability using maximum entropy modeling. Sequence diversity analysis revealed a total of 188 genotyped alleles, with overall nucleotide diversity of 0.014 ± 0.007, indicating that the Mae Hong Son chicken population is genetically highly diverse, with 35 (M1-M35) haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken. During domestication in the past 200-300 years after the crossing of indigenous chickens and red junglefowl, the Mae Hong Son chicken has adapted to the highland environment and played a significant socio-cultural role in the Northern Thai community. The unique genetic fingerprint of the Mae Hong Son chicken, retaining a high level of genetic variability that includes a dynamic demographic and domestication history, as well as a range of ecological factors, might reshape the adaptation of this breed under selective pressure.
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Affiliation(s)
- Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Aingorn Chaiyes
- School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi 11120, Thailand;
| | - Hina Ali
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Surachai Piangporntip
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- School of Integrated Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Bureau of Conservation and Research, Zoological Park Organization of Thailand, Bangkok 10300, Thailand
| | - Nattakan Ariyaraphong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Worawit Thienpreecha
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Wannapa Wannakan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Autchariyapron Mungmee
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Kittipong Jaisamut
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Warong Suksavate
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | | | - Mitsuo Nunome
- Department of Zoology, Faculty of Science, Okayama University of Science, Ridai-cho 1-1, Kita-ku, Okayama 700-0005, Japan;
| | - Wiyada Chamchumroon
- Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok 10900, Thailand;
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Republic of Korea
| | - Aniroot Nuangmek
- Mae Hong Son Provincial Livestock Office, Department of Livestock Development, Ministry of Agriculture and Cooperatives, Mae Hong Son 58000, Thailand;
| | - Yoichi Matsuda
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- School of Integrated Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
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Pan Y, Wang Y, McGregor C, Liu S, Luan F, Gao M, Weng Y. Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1-21. [PMID: 31768603 DOI: 10.1007/s00122-019-03481-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 11/11/2019] [Indexed: 05/28/2023]
Abstract
The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.
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Affiliation(s)
- Yupeng Pan
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yuhui Wang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Cecilia McGregor
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Shi Liu
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Feishi Luan
- College of Horticulture and, Landscape Architecture at Northeast Agricultural University, Harbin, 150030, China
| | - Meiling Gao
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Yiqun Weng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, 1575 Linden Dr., Madison, WI, 53706, USA.
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Kumari R, Wankhede DP, Bajpai A, Maurya A, Prasad K, Gautam D, Rangan P, Latha M, John K. J, A. S, Bhat KV, Gaikwad AB. Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications. PLoS One 2019; 14:e0226002. [PMID: 31834893 PMCID: PMC6910694 DOI: 10.1371/journal.pone.0226002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 11/18/2019] [Indexed: 11/23/2022] Open
Abstract
Black pepper is one of the most valued and widely used spices in the world and dominates multi-billion dollar global spices trade. India is amongst the major producers, consumers and exporters of black pepper. In spite of its commercial and cultural importance, black pepper has received meagre attention in terms of generation of genomic resources. Availability of markers distributed throughout the genome would facilitate and accelerate genetic studies, QTL identification, genetic enhancement and crop improvement in black pepper. In this perspective, the sequence information from the recently sequenced black pepper (Piper nigrum) genome has been used for identification and characterisation of Simple Sequence Repeats (SSRs). Total 69,126 SSRs were identified from assembled genomic sequence of P. nigrum. The SSR frequency was 158 per MB making it, one SSR for every 6.3 kb in the assembled genome. Among the different types of microsatellite repeat motifs, dinucleotides were the most abundant (48.6%), followed by trinucleotide (23.7%) and compound repeats (20.62%). A set of 85 SSRs were used for validation, of which 74 produced amplification products of expected size. Genetic diversity of 30 black pepper accessions using 50 SSRs revealed four distinct clusters. Further, the cross species transferability of the SSRs was checked in nine other Piper species. Out of 50 SSRs used, 19 and 31 SSRs were amplified in nine and seven species, respectively. Thus the identified SSRs may have application in other species of the genus Piper where genome sequence is not available yet. Present study reports the first NGS based genomic SSRs in black pepper and thus constitute a valuable resource for a whole fleet of applications in genetics and plant breeding studies such as genetic map construction, QTL identification, map-based gene cloning, marker-assisted selection and evolutionary studies in Piper nigrum and related species.
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Affiliation(s)
- Ratna Kumari
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Akansha Bajpai
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Avantika Maurya
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kartikay Prasad
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dikshant Gautam
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Parimalan Rangan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - M. Latha
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Joseph John K.
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Suma A.
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kangila V. Bhat
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ambika B. Gaikwad
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
- * E-mail:
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Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon. Int J Mol Sci 2019; 20:ijms20215392. [PMID: 31671884 PMCID: PMC6862219 DOI: 10.3390/ijms20215392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/21/2019] [Accepted: 10/26/2019] [Indexed: 12/30/2022] Open
Abstract
Watermelon is a good source of citrulline, a non-protein amino acid. Citrulline has several therapeutic and clinical implications as it produces nitric oxide via arginine. In plants, citrulline plays a pivotal role in nitrogen transport and osmoprotection. The purpose of this study was to identify single nucleotide polymorphism (SNP) markers associated with citrulline metabolism using a genome-wide association study (GWAS) and understand the role of citrulline in watermelon domestication. A watermelon collection consisting of 187 wild, landraces, and cultivated accessions was used to estimate citrulline content. An association analysis involved a total of 12,125 SNPs with a minor allele frequency (MAF) >0.05 in understanding the population structure and phylogeny in light of citrulline accumulation. Wild egusi types and landraces contained low to medium citrulline content, whereas cultivars had higher content, which suggests that obtaining higher content of citrulline is a domesticated trait. GWAS analysis identified candidate genes (ferrochelatase and acetolactate synthase) showing a significant association of SNPs with citrulline content. Haplotype networking indicated positive selection from wild to domesticated watermelon. To our knowledge, this is the first study showing genetic regulation of citrulline variation in plants by using a GWAS strategy. These results provide new insights into the citrulline metabolism in plants and the possibility of incorporating high citrulline as a trait in watermelon breeding programs.
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Lee KJ, Lee JR, Sebastin R, Shin MJ, Kim SH, Cho GT, Hyun DY. Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm. Genes (Basel) 2019; 10:genes10100822. [PMID: 31635343 PMCID: PMC6826620 DOI: 10.3390/genes10100822] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/23/2019] [Accepted: 10/15/2019] [Indexed: 12/25/2022] Open
Abstract
Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.
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Affiliation(s)
- Kyung Jun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea.
| | - Jung-Ro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea.
| | - Raveendar Sebastin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea.
| | - Myoung-Jae Shin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea.
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea.
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea.
| | - Do Yoon Hyun
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), RDA, Jeonju 54874, Korea.
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10
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Subburaj S, Lee K, Jeon Y, Tu L, Son G, Choi S, Lim YP, McGregor C, Lee GJ. Whole genome resequencing of watermelons to identify single nucleotide polymorphisms related to flesh color and lycopene content. PLoS One 2019; 14:e0223441. [PMID: 31596903 PMCID: PMC6785133 DOI: 10.1371/journal.pone.0223441] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 09/20/2019] [Indexed: 12/30/2022] Open
Abstract
Cultivated watermelon (Citrullus lanatus) is one of the most important food crops in the Cucurbitaceae family. Diversification after domestication has led cultivated watermelons to exhibit diverse fruit flesh colors, including red, yellow, and orange. Recently, there has been increased interest in red-fleshed watermelons because they contain the antioxidant cis-isomeric lycopene. We performed whole genome resequencing (WGRS) of 24 watermelons with different flesh colors to identify single-nucleotide polymorphisms (SNPs) related to high lycopene content. The resequencing data revealed 203,894-279,412 SNPs from read mapping between inbred lines and the 97103 reference genome. In total, 295,065 filtered SNPs were identified, which had an average polymorphism information content of 0.297. Most of these SNPs were intergenic (90.1%) and possessed a transversion (Tv) rate of 31.64%. Overall, 2,369 SNPs were chosen at 0.5 Mb physical intervals to analyze genetic diversity across the 24 inbred lines. A neighbor-joining dendrogram and principal coordinate analysis (PCA) based on the 2,369 SNPs revealed that the 24 inbred lines could be grouped into high and low lycopene-type watermelons. In addition, we analyzed SNPs that could discriminate high lycopene content, red-fleshed watermelon from low lycopene, yellow or orange watermelon inbred lines. For validation, 19 SNPs (designated as WMHL1-19) were chosen randomly, and cleavage amplified polymorphic sequence (CAPS) markers were designed. Genotyping of the above 24 lines and 12 additional commercial cultivars using WMHL1-19 CAPS markers resulted in match rates of over 0.92 for most validated markers in correlation with the flesh color phenotypes. Our results provide valuable genomic information regarding the high lycopene content phenotype of red-fleshed cultivated watermelons, and the identified SNPs will be useful for the development of molecular markers in the marker-assisted breeding of watermelons with high lycopene content.
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Affiliation(s)
- Saminathan Subburaj
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Kayoun Lee
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Yongsam Jeon
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Luhua Tu
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Gilwoo Son
- Breeding Institute, Hyundai Seed Co Ltd., Yeoju, Gyeonggi, Republic of Korea
| | - SuBok Choi
- Asia Seed, Co., Ltd., Seoul, Republic of Korea
| | - Yong-Pyo Lim
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA, United States of America
| | - Geung-Joo Lee
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
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Wang Y, Guo S, Tian S, Zhang J, Ren Y, Sun H, Gong G, Zhang H, Xu Y. Abscisic acid pathway involved in the regulation of watermelon fruit ripening and quality trait evolution. PLoS One 2017; 12:e0179944. [PMID: 28662086 PMCID: PMC5491074 DOI: 10.1371/journal.pone.0179944] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/07/2017] [Indexed: 01/09/2023] Open
Abstract
Watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) is a non-climacteric fruit. The modern sweet-dessert watermelon is the result of years of cultivation and selection for fruits with desirable qualities. To date, the mechanisms of watermelon fruit ripening, and the role of abscisic acid (ABA) in this process, has not been well understood. We quantified levels of free and conjugated ABA contents in the fruits of cultivated watermelon (97103; C. lanatus subsp. vulgaris), semi-wild germplasm (PI179878; C. lanatus subsp. mucosospermus), and wild germplasm (PI296341-FR; C. lanatus subsp. lanatus). Results showed that ABA content in the fruits of 97103 and PI179878 increased during fruit development and ripening, but maintained a low steady state in the center flesh of PI296341-FR fruits. ABA levels in fruits were highest in 97103 and lowest in PI296341-FR, but no obvious differences in ABA levels were observed in seeds of these lines. Examination of 31 representative watermelon accessions, including different C. lanatus subspecies and ancestral species, showed a correlation between soluble solids content (SSC) and ABA levels in ripening fruits. Furthermore, injection of exogenous ABA or nordihydroguaiaretic acid (NDGA) into 97103 fruits promoted or inhibited ripening, respectively. Transcriptomic analyses showed that the expression levels of several genes involved in ABA metabolism and signaling, including Cla009779 (NCED), Cla005404 (NCED), Cla020673 (CYP707A), Cla006655 (UGT) and Cla020180 (SnRK2), varied significantly in cultivated and wild watermelon center flesh. Three SNPs (-738, C/A; -1681, C/T; -1832, G/T) in the promoter region of Cla020673 (CYP707A) and one single SNP (-701, G/A) in the promoter of Cla020180 (SnRK2) exhibited a high level of correlation with SSC variation in the 100 tested accessions. Our results not only demonstrate for the first time that ABA is involved in the regulation of watermelon fruit ripening, but also provide insights into the evolutionary mechanisms of this phenomenon.
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Affiliation(s)
- Yanping Wang
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Shaogui Guo
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Shouwei Tian
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Jie Zhang
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Yi Ren
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Honghe Sun
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Guoyi Gong
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Haiying Zhang
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
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Zhu H, Song P, Koo DH, Guo L, Li Y, Sun S, Weng Y, Yang L. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis. BMC Genomics 2016; 17:557. [PMID: 27495254 PMCID: PMC4974753 DOI: 10.1186/s12864-016-2870-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/01/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections. RESULTS A total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis clustered in another group. Furthermore, structure analysis was consistent with the dendrogram indicating the 134 watermelon accessions were classified into two populations. CONCLUSION The large number of genome wide SSR markers developed herein from the watermelon genome provides a valuable resource for genetic map construction, QTL exploration, map-based gene cloning and marker-assisted selection in watermelon which has a very narrow genetic base and extremely low polymorphism among cultivated lines. Furthermore, the cross-species transferable SSR markers identified herein should also have practical uses in many applications in species of Cucurbitaceae family whose whole genome sequences are not yet available.
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Affiliation(s)
- Huayu Zhu
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Pengyao Song
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Dal-Hoe Koo
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
| | - Luqin Guo
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Yanman Li
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Shouru Sun
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- US Department of Agriculture/Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI 53706 USA
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
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Grumet R, Colle M. Genomic Analysis of Cucurbit Fruit Growth. GENETICS AND GENOMICS OF CUCURBITACEAE 2016. [DOI: 10.1007/7397_2016_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Paris HS. Origin and emergence of the sweet dessert watermelon, Citrullus lanatus. ANNALS OF BOTANY 2015; 116:133-48. [PMID: 26141130 PMCID: PMC4512189 DOI: 10.1093/aob/mcv077] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/16/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Watermelons, Citrullus species (Cucurbitaceae), are native to Africa and have been cultivated since ancient times. The fruit flesh of wild watermelons is watery, but typically hard-textured, pale-coloured and bland or bitter. The familiar sweet dessert watermelons, C. lanatus, featuring non-bitter, tender, well-coloured flesh, have a narrow genetic base, suggesting that they originated from a series of selection events in a single ancestral population. The objective of the present investigation was to determine where dessert watermelons originated and the time frame during which sweet dessert watermelons emerged. KEY FINDINGS Archaeological remains of watermelons, mostly seeds, that date from 5000 years ago have been found in northeastern Africa. An image of a large, striped, oblong fruit on a tray has been found in an Egyptian tomb that dates to at least 4000 years ago. The Greek word pepon, Latin pepo and Hebrew avattiah of the first centuries CE were used for the same large, thick-rinded, wet fruit which, evidently, was the watermelon. Hebrew literature from the end of the second century CE and Latin literature from the beginning of the sixth century CE present watermelons together with three sweet fruits: figs, table grapes and pomegranates. Wild and primitive watermelons have been observed repeatedly in Sudan and neighbouring countries of northeastern Africa. CONCLUSIONS The diverse evidence, combined, indicates that northeastern Africa is the centre of origin of the dessert watermelon, that watermelons were domesticated for water and food there over 4000 years ago, and that sweet dessert watermelons emerged in Mediterranean lands by approximately 2000 years ago. Next-generation ancient-DNA sequencing and state-of-the-art genomic analysis offer opportunities to rigorously assess the relationships among ancient and living wild and primitive watermelons from northeastern Africa, modern sweet dessert watermelons and other Citrullus taxa.
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Affiliation(s)
- Harry S Paris
- Institute of Plant Sciences, Agricultural Research Organization, Newe Ya'ar Research Center, P. O. Box 1021, Ramat Yishay 30-095, Israel
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