1
|
Guo S, Tian M, Du H, Liu S, Yu R, Shen H. Quantitative Trait Loci Mapping and Comparative Transcriptome Analysis of Fruit Weight (FW) in Watermelon ( Citrullus lanatus L.). Genes (Basel) 2024; 15:933. [PMID: 39062712 PMCID: PMC11276344 DOI: 10.3390/genes15070933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The watermelon (Citrullus lanatus L.) holds substantial economic value as a globally cultivated horticultural crop. However, the genetic architecture of watermelon fruit weight (FW) remains poorly understood. In this study, we used sh14-11 with small fruit and N14 with big fruit to construct 100 recombinant inbred lines (RILs). Based on whole-genome resequencing (WGR), 218,127 single nucleotide polymorphisms (SNPs) were detected to construct a high-quality genetic map. After quantitative trait loci (QTL) mapping, a candidate interval of 31-38 Mb on chromosome 2 was identified for FW. Simultaneously, the bulked segregant analysis (BSA) in the F2 population corroborated the identification of the same interval, encompassing the homologous gene linked to the known FW-related gene fas. Additionally, RNA-seq was carried out across 11 tissues from sh14-11 and N14, revealing expression profiles that identified 1695 new genes and corrected the annotation of 2941 genes. Subsequent differential expression analysis unveiled 8969 differentially expressed genes (DEGs), with 354 of these genes exhibiting significant differences across four key developmental stages. The integration of QTL mapping and differential expression analysis facilitated the identification of 14 FW-related genes, including annotated TGA and NAC transcription factors implicated in fruit development. This combined approach offers valuable insights into the genetic basis of FW, providing crucial resources for enhancing watermelon cultivation.
Collapse
Affiliation(s)
- Song Guo
- Horticulture College, China Agricultural University, Beijing 100193, China;
| | - Mei Tian
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Huiying Du
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Shengfeng Liu
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Rong Yu
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Huolin Shen
- Horticulture College, China Agricultural University, Beijing 100193, China;
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Hassett K, Muria-Gonzalez MJ, Turner A, McLean MS, Wallwork H, Martin A, Ellwood SR. Widespread genetic heterogeneity and genotypic grouping associated with fungicide resistance among barley spot form net blotch isolates in Australia. G3 (BETHESDA, MD.) 2023; 13:jkad076. [PMID: 37002913 PMCID: PMC10151411 DOI: 10.1093/g3journal/jkad076] [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: 02/13/2023] [Revised: 02/13/2023] [Accepted: 03/10/2023] [Indexed: 04/04/2023]
Abstract
Spot form net blotch, caused by Pyrenophora teres f. maculata, is a major foliar disease of barley worldwide. Knowledge of the pathogen's genetic diversity and population structure is critical for a better understanding of inherent evolutionary capacity and for the development of sustainable disease management strategies. Genome-wide, single nucleotide polymorphism data of 254 Australian isolates revealed genotypic diversity and an absence of population structure, either between states, or between fields and cultivars in different agro-ecological zones. This indicates there is little geographical isolation or cultivar directional selection and that the pathogen is highly mobile across the continent. However, two cryptic genotypic groups were found only in Western Australia, predominantly associated with genes involved in fungicide resistance. The findings in this study are discussed in the context of current cultivar resistance and the pathogen's adaptive potential.
Collapse
Affiliation(s)
- Kealan Hassett
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | | | - Aleesha Turner
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Mark S McLean
- Field Crops Pathology, Agriculture Victoria, Horsham, Victoria 3401, Australia
| | - Hugh Wallwork
- Cereal Pathology Laboratory, South Australian Research and Development Institute, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland 4350, Australia
| | - Simon R Ellwood
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| |
Collapse
|
4
|
Semalaiyappan J, Selvanayagam S, Rathore A, Gupta SK, Chakraborty A, Gujjula KR, Haktan S, Viswanath A, Malipatil R, Shah P, Govindaraj M, Ignacio JC, Reddy S, Singh AK, Thirunavukkarasu N. Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding. FRONTIERS IN PLANT SCIENCE 2023; 13:1068883. [PMID: 36704175 PMCID: PMC9871632 DOI: 10.3389/fpls.2022.1068883] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Pearl millet is a crucial nutrient-rich staple food in Asia and Africa and adapted to the climate of semi-arid topics. Since the genomic resources in pearl millet are very limited, we have developed a brand-new mid-density 4K SNP panel and demonstrated its utility in genetic studies. A set of 4K SNPs were mined from 925 whole-genome sequences through a comprehensive in-silico pipeline. Three hundred and seventy-three genetically diverse pearl millet inbreds were genotyped using the newly-developed 4K SNPs through the AgriSeq Targeted Genotyping by Sequencing technology. The 4K SNPs were uniformly distributed across the pearl millet genome and showed considerable polymorphism information content (0.23), genetic diversity (0.29), expected heterozygosity (0.29), and observed heterozygosity (0.03). The SNP panel successfully differentiated the accessions into two major groups, namely B and R lines, through genetic diversity, PCA, and structure models as per their pedigree. The linkage disequilibrium (LD) analysis showed Chr3 had higher LD regions while Chr1 and Chr2 had more low LD regions. The genetic divergence between the B- and R-line populations was 13%, and within the sub-population variability was 87%. In this experiment, we have mined 4K SNPs and optimized the genotyping protocol through AgriSeq technology for routine use, which is cost-effective, fast, and highly reproducible. The newly developed 4K mid-density SNP panel will be useful in genomics and molecular breeding experiments such as assessing the genetic diversity, trait mapping, backcross breeding, and genomic selection in pearl millet.
Collapse
Affiliation(s)
- Janani Semalaiyappan
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | - Sivasubramani Selvanayagam
- Accelerated Crop Improvement, International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- Excellence in Breeding (EiB) Platform, The International Maize and Wheat Improvement Center (CIMMYT), El Batán, Mexico
| | - SK. Gupta
- Accelerated Crop Improvement, International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Animikha Chakraborty
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | | | - Suren Haktan
- Bioinformatics, Thermo Fisher Scientific, Austin, TX, United States
| | - Aswini Viswanath
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | - Renuka Malipatil
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | - Priya Shah
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | | | - John Carlos Ignacio
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, United States
| | - Sanjana Reddy
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | | | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| |
Collapse
|
5
|
Miura I, Shams F, Jeffries DL, Katsura Y, Mawaribuchi S, Perrin N, Ito M, Ogata M, Ezaz T. Identification of ancestral sex chromosomes in the frog Glandirana rugosa bearing XX-XY and ZZ-ZW sex-determining systems. Mol Ecol 2022; 31:3859-3870. [PMID: 35691011 DOI: 10.1111/mec.16551] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/03/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
Abstract
Sex chromosomes constantly exist in a dynamic state of evolution: rapid turnover and change of heterogametic sex during homomorphic state, and often stepping out to a heteromorphic state followed by chromosomal decaying. However, the forces driving these different trajectories of sex chromosome evolution are still unclear. The Japanese frog Glandirana rugosa is one taxon well suited to the study on these driving forces. The species has two different heteromorphic sex chromosome systems, XX-XY and ZZ-ZW, which are separated in different geographic populations. Both XX-XY and ZZ-ZW sex chromosomes are represented by chromosome 7 (2n = 26). Phylogenetically, these two systems arose via hybridization between two ancestral lineages of West Japan and East Japan populations, of which sex chromosomes are homomorphic in both sexes and to date have not yet been identified. Identification of the sex chromosomes will give us important insight into the mechanisms of sex chromosome evolution in this species. Here, we used a high-throughput genomic approach to identify the homomorphic XX-XY sex chromosomes in both ancestral populations. Sex-linked DNA markers of West Japan were aligned to chromosome 1, whereas those of East Japan were aligned to chromosome 3. These results reveal that at least two turnovers across three different sex chromosomes 1, 3 and 7 occurred during evolution of this species. This finding raises the possibility that cohabitation of the two different sex chromosomes from ancestral lineages induced turnover to another new one in their hybrids, involving transition of heterogametic sex and evolution from homomorphy to heteromorphy.
Collapse
Affiliation(s)
- Ikuo Miura
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan.,Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Foyez Shams
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Daniel Lee Jeffries
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Yukako Katsura
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Shuuji Mawaribuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Michihiko Ito
- School of Science, Kitasato University, Sagamihara, Japan
| | - Mitsuaki Ogata
- Preservation and Research Center, City of Yokohama, Yokohama, Japan
| | - Tariq Ezaz
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan.,Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| |
Collapse
|
6
|
Panthum T, Jaisamut K, Singchat W, Ahmad SF, Kongkaew L, Wongloet W, Dokkaew S, Kraichak E, Muangmai N, Duengkae P, Srikulnath K. Something Fishy about Siamese Fighting Fish (Betta splendens) Sex: Polygenic Sex Determination or a Newly Emerged Sex-Determining Region? Cells 2022; 11:cells11111764. [PMID: 35681459 PMCID: PMC9179492 DOI: 10.3390/cells11111764] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 12/04/2022] Open
Abstract
Fishes provide a unique and intriguing model system for studying the genomic origin and evolutionary mechanisms underlying sex determination and high sex-chromosome turnover. In this study, the mode of sex determination was investigated in Siamese fighting fish, a species of commercial importance. Genome-wide SNP analyses were performed on 75 individuals (40 males and 35 females) across commercial populations to determine candidate sex-specific/sex-linked loci. In total, 73 male-specific loci were identified and mapped to a 5.6 kb region on chromosome 9, suggesting a putative male-determining region (pMDR) containing localized dmrt1 and znrf3 functional sex developmental genes. Repeat annotations of the pMDR revealed an abundance of transposable elements, particularly Ty3/Gypsy and novel repeats. Remarkably, two out of the 73 male-specific loci were located on chromosomes 7 and 19, implying the existence of polygenic sex determination. Besides male-specific loci, five female-specific loci on chromosome 9 were also observed in certain populations, indicating the possibility of a female-determining region and the polygenic nature of sex determination. An alternative explanation is that male-specific loci derived from other chromosomes or female-specific loci in Siamese fighting fish recently emerged as new sex-determining loci during domestication and repeated hybridization.
Collapse
Affiliation(s)
- Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.J.); (W.S.); (S.F.A.); (L.K.); (W.W.); (E.K.); (N.M.); (P.D.)
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Kitipong Jaisamut
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.J.); (W.S.); (S.F.A.); (L.K.); (W.W.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.J.); (W.S.); (S.F.A.); (L.K.); (W.W.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.J.); (W.S.); (S.F.A.); (L.K.); (W.W.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Lalida Kongkaew
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.J.); (W.S.); (S.F.A.); (L.K.); (W.W.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.J.); (W.S.); (S.F.A.); (L.K.); (W.W.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Sahabhop Dokkaew
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand;
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.J.); (W.S.); (S.F.A.); (L.K.); (W.W.); (E.K.); (N.M.); (P.D.)
- Department of Botany, Kasetsart University, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.J.); (W.S.); (S.F.A.); (L.K.); (W.W.); (E.K.); (N.M.); (P.D.)
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.J.); (W.S.); (S.F.A.); (L.K.); (W.W.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.J.); (W.S.); (S.F.A.); (L.K.); (W.W.); (E.K.); (N.M.); (P.D.)
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, (CASTNAR, NRU-KU, Thailand), Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, Kagamiyama, Higashihiroshima 739-8527, Japan
- Correspondence:
| |
Collapse
|
7
|
Nguyen DHM, Ponjarat J, Laopichienpong N, Panthum T, Singchat W, Ahmad SF, Kraichak E, Muangmai N, Duengkae P, Peyachoknagul S, Na-Nakorn U, Srikulnath K. Genome-Wide SNP Analysis of Hybrid Clariid Fish Reflects the Existence of Polygenic Sex-Determination in the Lineage. Front Genet 2022; 13:789573. [PMID: 35186027 PMCID: PMC8851383 DOI: 10.3389/fgene.2022.789573] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/10/2022] [Indexed: 12/17/2022] Open
Abstract
The African catfish (Clarias gariepinus) may exhibit the co-existence of XX/XY and ZZ/ZW sex-determination systems (SDSs). However, the SDS of African catfish might be influenced by a polygenic sex-determination (PSD) system, comprising multiple independently segregating sex “switch” loci to determine sex within a species. Here, we aimed to detect the existence of PSD using hybrid. The hybrid produced by crossing male African catfish with female bighead catfish (C. macrocephalus, XX/XY) is a good animal model to study SDSs. Determining the SDS of hybrid catfish can help in understanding the interactions between these two complex SDS systems. Using the genotyping-by-sequencing “DART-seq” approach, we detected seven moderately male-linked loci and seventeen female-linked loci across all the examined hybrid specimens. Most of these loci were not sex-linked in the parental species, suggesting that the hybrid exhibits a combination of different alleles. Annotation of the identified sex-linked loci revealed the presence of one female-linked locus homologous with the B4GALNT1 gene, which is involved in the spermatogenesis pathway and hatchability. However, this locus was not sex-linked in the parental species, and the African catfish might also exhibit PSD.
Collapse
Affiliation(s)
- Dung Ho My Nguyen
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Jatupong Ponjarat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Nararat Laopichienpong
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | | | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan
- *Correspondence: Kornsorn Srikulnath,
| |
Collapse
|
8
|
The Snakeskin Gourami (Trichopodus pectoralis) Tends to Exhibit XX/XY Sex Determination. FISHES 2021. [DOI: 10.3390/fishes6040043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The snakeskin gourami (Trichopodus pectoralis) has a high meat yield and is one of the top five aquaculture freshwater fishes in Thailand. The species is not externally sexually dimorphic, and its sex determination system is unknown. Understanding the sex determination system of this species will contribute to its full-scale commercialization. In this study, a cytogenetic analysis did not reveal any between-sex differences in chromosomal patterns. However, we used genotyping-by-sequencing to identify 4 male-linked loci and 1 female-linked locus, indicating that the snakeskin gourami tends to exhibit an XX/XY sex determination system. However, we did not find any male-specific loci after filtering the loci for a ratio of 100:0 ratio of males:females. This suggests that the putative Y chromosome is young and that the sex determination region is cryptic. This approach provides solid information that can help identify the sex determination mechanism and potential sex determination regions in the snakeskin gourami, allowing further investigation of genetic improvements in the species.
Collapse
|
9
|
Proft KM, Bateman BL, Johnson CN, Jones ME, Pauza M, Burridge CP. The effects of weather variability on patterns of genetic diversity in Tasmanian bettongs. Mol Ecol 2021; 30:1777-1790. [PMID: 33590590 DOI: 10.1111/mec.15847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/04/2021] [Accepted: 02/11/2021] [Indexed: 12/01/2022]
Abstract
While the effects of climate (long-term, prevailing weather) on species abundance, range and genetic diversity have been widely studied, short-term, localized variations in atmospheric conditions (i.e., weather) can also rapidly alter species' geographical ranges and population sizes, but little is known about how they affect genetic diversity. We investigated the relationship between weather and range-wide genetic diversity in a marsupial, Bettongia gaimardi, using dynamic species distribution models (SDMs). Genetic diversity was lower in parts of the range where the weather-based SDM predicted high variability in probability of B. gaimardi occurrence during 1950-2009. This is probably an effect of lower population sizes and extinction-recolonization cycles in places with highly variable weather. Spatial variation in genetic diversity was also better predicted by mean probabilities of B. gaimardi occurrence from weather- than climate-based SDMs. Our results illustrate the importance of weather in driving population dynamics and species distributions on decadal timescales and thereby in affecting genetic diversity. Modelling the links between changing weather patterns, species distributions and genetic diversity will allow researchers to better forecast biological impacts of climate change.
Collapse
Affiliation(s)
- Kirstin M Proft
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Christopher N Johnson
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania, Australia
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Matthew Pauza
- Biosecurity Tasmania, Department of Primary Industries, Parks, Water and Environment, Hobart, Tasmania, Australia
| | | |
Collapse
|
10
|
Nguyen DHM, Panthum T, Ponjarat J, Laopichienpong N, Kraichak E, Singchat W, Ahmad SF, Muangmai N, Peyachoknagul S, Na-Nakorn U, Srikulnath K. An Investigation of ZZ/ZW and XX/XY Sex Determination Systems in North African Catfish ( Clarias gariepinus, ). Front Genet 2021; 11:562856. [PMID: 33584785 PMCID: PMC7874028 DOI: 10.3389/fgene.2020.562856] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022] Open
Abstract
An investigation of sex-specific loci may provide important insights into fish sex determination strategies. This may be useful for biotechnological purposes, for example, to produce all-male or all-female fish for commercial breeding. The North African catfish species, Clarias gariepinus, has been widely adopted for aquaculture because its superior growth and disease resistance render the species suitable for hybridization with other catfish to improve the productivity and quality of fish meat. This species has either a ZZ/ZW or XX/XY sex determination system. Here, we investigate and characterize these systems using high-throughput genome complexity reduction sequencing as Diversity Arrays Technology. This approach was effective in identifying moderately sex-linked loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 30 perfectly sexed individuals of C. gariepinus. However, SNPs based markers were not found in this study. In total, 41 loci met the criteria for being moderately male-linked (with male vs. female ratios 80:20 and 70:30), while 25 loci were found to be moderately linked to female sex. No strictly male- or female-linked loci were detected. Seven moderately male-linked loci were partially homologous to some classes of transposable elements and three moderately male-linked loci were partially homologous to functional genes. Our data showed that the male heterogametic XX/XY sex determination system should co-exist with the ZZ/ZW system in C. gariepinus. Our finding of the co-existence of XX/XY and ZZ/ZW systems can be applied to benefit commercial breeding of this species in Thailand. This approach using moderately sex-linked loci provides a solid baseline for revealing sex determination mechanisms and identify potential sex determination regions in catfish, allowing further investigation of genetic improvements in breeding programs.
Collapse
Affiliation(s)
- Dung Ho My Nguyen
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Jatupong Ponjarat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | | | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand.,Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand.,Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan
| |
Collapse
|
11
|
Valdisser PAMR, Müller BSF, de Almeida Filho JE, Morais Júnior OP, Guimarães CM, Borba TCO, de Souza IP, Zucchi MI, Neves LG, Coelho ASG, Brondani C, Vianello RP. Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:574674. [PMID: 33343591 PMCID: PMC7738703 DOI: 10.3389/fpls.2020.574674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/22/2020] [Indexed: 05/26/2023]
Abstract
Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans' yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r 2 sv ), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling ∼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed ∼220 genomic regions containing ∼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (∼221 QTLs; 650 genes; r 2 from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean.
Collapse
Affiliation(s)
- Paula Arielle Mendes Ribeiro Valdisser
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, UNICAMP, Campinas, Brazil
| | - Bárbara S. F. Müller
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | | | | | | | - Tereza C. O. Borba
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
| | - Isabela Pavanelli de Souza
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
- Postgraduate Program in Biological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Maria Imaculada Zucchi
- Genetics and Molecular Biology Graduate Program, Institute of Biology, UNICAMP, Campinas, Brazil
- Agribusiness Technology Agency of São Paulo State, Agriculture and Food Supply Secretary of São Paulo, Piracicaba, Brazil
| | | | | | - Claudio Brondani
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
| | | |
Collapse
|
12
|
Koomgun T, Laopichienpong N, Singchat W, Panthum T, Phatcharakullawarawat R, Kraichak E, Sillapaprayoon S, Ahmad SF, Muangmai N, Peyachoknagul S, Duengkae P, Ezaz T, Srikulnath K. Genome Complexity Reduction High-Throughput Genome Sequencing of Green Iguana ( Iguana iguana) Reveal a Paradigm Shift in Understanding Sex-Chromosomal Linkages on Homomorphic X and Y Sex Chromosomes. Front Genet 2020; 11:556267. [PMID: 33193634 PMCID: PMC7606854 DOI: 10.3389/fgene.2020.556267] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/24/2020] [Indexed: 12/27/2022] Open
Abstract
The majority of lizards classified in the superfamily Iguanoidea have an XX/XY sex-determination system in which sex-chromosomal linkage shows homology with chicken (Gallus gallus) chromosome 15 (GGA15). However, the genomics of sex chromosomes remain largely unexplored owing to the presence of homomorphic sex chromosomes in majority of the species. Recent advances in high-throughput genome complexity reduction sequencing provide an effective approach to the identification of sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in Iguanoidea. In this study, we applied Diversity Arrays Technology (DArTseqTM) in 29 phenotypic sex assignments (14 males and 15 females) of green iguana (Iguana iguana). We confirmed a male heterogametic (XX/XY) sex determination mode in this species, identifying 29 perfectly sex-linked SNP/PA loci and 164 moderately sex-linked SNP/PA loci, providing evidence probably indicative of XY recombination. Three loci from among the perfectly sex-linked SNP/PA loci showed partial homology with several amniote sex chromosomal linkages. The results support the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex-chromosomal linkages. However, only one locus among the moderately sex-linked loci showed homology with GGA15, which suggests that the specific region homologous to GGA15 was located outside the non-recombination region but in close proximity to this region of the sex chromosome in green iguana. Therefore, the location of GGA15 might be further from the putative sex-determination locus in green iguana. This is a paradigm shift in understanding linkages on homomorphic X and Y sex chromosomes. The DArTseq platform provides an easy-to-use strategy for future research on the evolution of sex chromosomes in Iguanoidea, particularly for non-model species with homomorphic or highly cryptic sex chromosomes.
Collapse
Affiliation(s)
- Tassika Koomgun
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | | | | | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources, National Research University, Kasetsart University, Bangkok, Thailand.,Center of Excellence on Agricultural Biotechnology, Bangkok, Thailand.,Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University, Bangkok, Thailand
| |
Collapse
|
13
|
Xia F, Ouyang Y. Recurrent breakdown and rebalance of segregation distortion in the genomes: battle for the transmission advantage. ABIOTECH 2020; 1:246-254. [PMID: 36304131 PMCID: PMC9590546 DOI: 10.1007/s42994-020-00023-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 05/28/2020] [Indexed: 01/25/2023]
Abstract
Mendel's laws state that each of the two alleles would segregate during gamete formation and show the same transmission ratio in the next generation. However, an unexpected biased allele transmission was first detected in Drosophila a century ago, and was subsequently observed in other animals, plants, and microorganisms. Such segregation distortion (SD) shows substantial effects in population structure and fitness of the progenies, which would ultimately lead to reproductive isolation and speciation. Here, we trace the early investigations on the violation of Mendelian genetic principle, which appears as a wide-existence phenomenon rather than a case of exception. The occurence of SD in the whole genome was observed in a number of plant species at the single- and multi-locus level. Biased transmission ratio might occur at meiosis stage due to asymmetric movement of the chromosome; transmission ratio advantage is also caused by interaction and battle between the alleles from respective genomes at the genetic and molecular level. The origin of a SD system is likely to be determined by coevolution of the killer and protector via recurrent breakdown or rebalance loop. These updated understandings also promote genetic improvement of hybrid crops.
Collapse
Affiliation(s)
- Fan Xia
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 China
| |
Collapse
|
14
|
Laopichienpong N, Kraichak E, Singchat W, Sillapaprayoon S, Muangmai N, Suntrarachun S, Baicharoen S, Peyachoknagul S, Chanhome L, Ezaz T, Srikulnath K. Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes. Genomics 2020; 113:624-636. [PMID: 33002626 DOI: 10.1016/j.ygeno.2020.09.058] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/10/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The W sex chromosome of the Siamese cobra (Naja kaouthia) contains a large number of repeats and shares amniote sex chromosomal linkages. Diversity Arrays Technology provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 sex-specific loci, 90 showed partial homology with sex chromosomes of several amniotes and 89 loci were homologous to transposable elements. Two loci were confirmed as W-specific nucleotides after PCR amplification. These loci might result from a sex chromosome differentiation process and involve putative sex-determination regions in the Siamese cobra. Sex-specific loci shared linkage homologies among amniote sex chromosomes, supporting an ancestral super-sex chromosome.
Collapse
Affiliation(s)
- Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, 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.
| | - Ekaphan Kraichak
- Department of Botany, Kasetsart University, Bangkok 10900, Thailand.
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, 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.
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, 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.
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Sunutcha Suntrarachun
- Snake Farm, Queen Saovabha Memorial Institute, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Sudarath Baicharoen
- Bureau of Conservation and Research, Zoological Park Organization under the Royal Patronage of His Majesty the King, Bangkok 10300, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
| | - Lawan Chanhome
- Snake Farm, Queen Saovabha Memorial Institute, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, 2617, Australia.
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, 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; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand, (CASTNAR, NRU-KU, Thailand); Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand; Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan.
| |
Collapse
|
15
|
Dadjo C, Nyende AB, Yao N, Kiplangat N, Assogbadjo AE. Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology. PLoS One 2020; 15:e0238984. [PMID: 32966312 PMCID: PMC7511007 DOI: 10.1371/journal.pone.0238984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 08/27/2020] [Indexed: 11/18/2022] Open
Abstract
Garcinia kola (Heckel) is a versatile tree indigenous to West and Central Africa. All parts of the tree have value in traditional medicine. Natural populations of the species have declined over the years due to overexploitation. Assessment of genetic diversity and population structure of G. kola is important for its management and conservation. The present study investigates the genetic diversity and population structure of G. kola populations in Benin using ultra-high-throughput diversity array technology (DArT) single nucleotide polymorphism (SNP) markers. From the 102 accessions sampled, two were excluded from the final dataset owing to poor genotyping coverage. A total of 43,736 SNPs were reported, of which 12,585 were used for analyses after screening with quality control parameters including Minor allele frequency (≥ 0.05), call rate (≥ 80%), reproducibility (≥ 95%), and polymorphic information content (≥ 1%). Analysis revealed low genetic diversity with expected heterozygosity per population ranging from 0.196 to 0.228. Pairwise F-statistics (FST) revealed low levels of genetic differentiation between populations while an Analysis of molecular variance (AMOVA) indicated that the majority of variation (97.86%) was within populations. Population structure analysis through clustering and discriminant analysis on principal component revealed two admixed clusters, implying little genetic structure. However, the model-based maximum likelihood in Admixture indicated only one genetic cluster. The present study indicated low genetic diversity of G. kola, and interventions are needed to be tailored towards its conservation.
Collapse
Affiliation(s)
- Colombe Dadjo
- Institute of Basic Sciences, Technology and Innovation, Pan African University, Nairobi, Kenya
- Laboratory of Applied Ecology, Faculty Agronomic Sciences, University of Abomey-Calavi, Cotonou, Rep. Benin
- * E-mail:
| | - Aggrey B. Nyende
- Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Nasser Yao
- Bioscience Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - Ngeno Kiplangat
- Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | - Achille E. Assogbadjo
- Laboratory of Applied Ecology, Faculty Agronomic Sciences, University of Abomey-Calavi, Cotonou, Rep. Benin
| |
Collapse
|
16
|
Aguirre-Liguori JA, Luna-Sánchez JA, Gasca-Pineda J, Eguiarte LE. Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize. Front Genet 2020; 11:870. [PMID: 33193568 PMCID: PMC7531271 DOI: 10.3389/fgene.2020.00870] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/16/2020] [Indexed: 12/21/2022] Open
Abstract
Massive parallel sequencing (MPS) is revolutionizing the field of molecular ecology by allowing us to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the economic and computational resources needed generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two simulated genomic datasets fitting a hierarchical structure, two extensive empirical genomic datasets, and a dataset comprising microsatellite information. For all datasets, we generated different subsampling designs by changing the number of loci, individuals, populations, and individuals per population to test for deviations in classic population genetics parameters (HS, FIS, FST). For the empirical datasets we also analyzed the effect of sampling design on landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling a different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. FIS was particularly sensitive to a low sampling of individuals in the simulated, genomic, and microsatellite datasets. For the empirical and simulated genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For the empirical datasets, we found that increasing the number of populations sampled was important in obtaining precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.
Collapse
Affiliation(s)
- Jonás A Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, United States
| | - Javier A Luna-Sánchez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jaime Gasca-Pineda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
17
|
Talamantes-Becerra B, Carling J, Kilian A, Georges A. Discovery of thermophilic Bacillales using reduced-representation genotyping for identification. BMC Microbiol 2020; 20:114. [PMID: 32404118 PMCID: PMC7222431 DOI: 10.1186/s12866-020-01800-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
Background This study demonstrates the use of reduced-representation genotyping to provide preliminary identifications for thermophilic bacterial isolates. The approach combines restriction enzyme digestion and PCR with next-generation sequencing to provide thousands of short-read sequences from across the bacterial genomes. Isolates were obtained from compost, hot water systems, and artesian bores of the Great Artesian Basin. Genomic DNA was double-digested with two combinations of restriction enzymes followed by PCR amplification, using a commercial provider of DArTseq™, Diversity Arrays Technology Pty Ltd. (Canberra, Australia). The resulting fragments which formed a reduced-representation of approximately 2.3% of the genome were sequenced. The sequence tags obtained were aligned against all available RefSeq bacterial genome assemblies by BLASTn to identify the nearest reference genome. Results Based on the preliminary identifications, a total of 99 bacterial isolates were identified to species level, from which 8 isolates were selected for whole-genome sequencing to assess the identification results. Novel species and strains were discovered within this set of isolates. The preliminary identifications obtained by reduced-representation genotyping, as well as identifications obtained by BLASTn alignment of the 16S rRNA gene sequence, were compared with those derived from the whole-genome sequence data, using the same RefSeq sequence database for the three methods. Identifications obtained with reduced-representation sequencing agreed with the identifications provided by whole-genome sequencing in 100% of cases. The identifications produced by BLASTn alignment of 16S rRNA gene sequence to the same database differed from those provided by whole-genome sequencing in 37.5% of cases, and produced ambiguous identifications in 50% of cases. Conclusions Previously, this method has been successfully demonstrated for use in bacterial identification for medical microbiology. This study demonstrates the first successful use of DArTseq™ for preliminary identification of thermophilic bacterial isolates, providing results in complete agreement with those obtained from whole-genome sequencing of the same isolates. The growing database of bacterial genome sequences provides an excellent resource for alignment of reduced-representation sequence data for identification purposes, and as the available sequenced genomes continue to grow, the technique will become more effective.
Collapse
Affiliation(s)
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Arthur Georges
- Institute of Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| |
Collapse
|
18
|
Mahboubi M, Mehrabi R, Naji AM, Talebi R. Whole-genome diversity, population structure and linkage disequilibrium analysis of globally diverse wheat genotypes using genotyping-by-sequencing DArTseq platform. 3 Biotech 2020; 10:48. [PMID: 32002339 PMCID: PMC6960278 DOI: 10.1007/s13205-019-2014-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/08/2019] [Indexed: 02/03/2023] Open
Abstract
In this study, 129 wheat genotypes from globally diverse origins were genotyped using DArTseq (SilicoDArT and SNP) markers. After filtering markers for quality-filtering, 14,270 SilicoDArTs and 6484 SNPs were retained and used for genetic diversity, population structure and linkage disequilibrium analyses. The highest number of SilicoDArT and SNP markers mapped on genome A and B compared to genome D. In both marker types, polymorphism information content (PIC) values ranged from 0.1 to 0.5, while > 0.80% of SilicoDArTs and > 0.44% SNPs showed PIC value more than median (0.25%). Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped wheat genotypes into three and four clusters, respectively. Principal component analysis and discriminant analysis of principal component results showed highly match with cluster and population structure analysis. Linkage disequilibrium (LD) was more extensive in both marker types, while graphical display of LD decay for both marker types showed that LD declined in the region close to 15 kbp, where r 2-values corresponded to r 2 = 0.16. Overall, our genetic diversity analysis showed high level of variation in studied wheat genotypes, even though there was no relationship between wheat grouping and origins. This might be attributed to admixture level that occurred during long-term natural selection of wheat genotypes in different parts of the world. Highly diverse wheat genotypes used in this study may possess unique genes and are useful sources in breeding programs to improve grain yield and quality.
Collapse
Affiliation(s)
- Mojgan Mahboubi
- College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, PO Box 8415683111, Isfahan, Iran
| | - Amir Mohammad Naji
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahed University, Tehran, Iran
| | - Reza Talebi
- College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| |
Collapse
|
19
|
Li B, Lu X, Gebremeskel H, Zhao S, He N, Yuan P, Gong C, Mohammed U, Liu W. Genetic Mapping and Discovery of the Candidate Gene for Black Seed Coat Color in Watermelon ( Citrullus lanatus). FRONTIERS IN PLANT SCIENCE 2020; 10:1689. [PMID: 32038674 PMCID: PMC6987421 DOI: 10.3389/fpls.2019.01689] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/29/2019] [Indexed: 06/01/2023]
Abstract
Seed coat color is an important trait highly affecting the seed quality and flesh appearance of watermelon (Citrullus lanatus). However, the molecular regulation mechanism of seed coat color in watermelon is still unclear. In the present study, genetic analysis was performed by evaluating F1, F2 and BC1 populations derived from two parental lines (9904 with light yellow seeds and Handel with black seeds), suggesting that a single dominant gene controls the black seed coat. The initial mapping result revealed a region of interest spanning 370 kb on chromosome 3. Genetic mapping with CAPS and SNP markers narrowed down the candidate region to 70.2 kb. Sequence alignment of the three putative genes in the candidate region suggested that there was a single-nucleotide insertion in the coding region of Cla019481 in 9904, resulting in a frameshift mutation and premature stop codon. The results indicated that Cla019481 named ClCS1 was the candidate gene for black seed coat color in watermelon. In addition, gene annotation revealed that Cla019481 encoded a polyphenol oxidase (PPO), which involved in the oxidation step of the melanin biosynthesis. This research finding will facilitate maker-assisted selection in watermelon and provide evidence for the study of black seed coat coloration in plants.
Collapse
|
20
|
Ren R, Xu J, Zhang M, Liu G, Yao X, Zhu L, Hou Q. Identification and Molecular Mapping of a Gummy Stem Blight Resistance Gene in Wild Watermelon ( Citrullus amarus) Germplasm PI 189225. PLANT DISEASE 2020; 104:16-24. [PMID: 31730411 DOI: 10.1094/pdis-04-19-0753-re] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Gummy stem blight (GSB), caused by Stagonosporopsis cucurbitacearum (syn. Didymella bryoniae), is a destructive foliar disease of watermelon in areas with hot and humid climates. The wild watermelon germplasm PI 189225 is a known source of resistance to GSB. The identification and use of molecular markers linked to resistance genes in the wild-type germplasm will speed up the introgression of GSB resistance into new watermelon varieties. An F2 segregating population was obtained from a cross between the resistant wild watermelon genotype PI 189225 and the susceptible genotype K3. The F2-derived F3 families were inoculated with a single isolate of S. cucurbitacearum (JS002) from Jiangsu Academy of Agricultural Sciences. The results of the genetic analysis demonstrated that GSB resistance in PI 189225 was controlled by a major quantitative trait locus (QTL), temporarily designated Qgsb8.1. Based on the results of bulk sergeant analysis and sequencing, one associated region spanning 5.7 Mb (10,358,659 to 16,101,517) on chromosome 8 was identified as responsible for the resistance to GSB using the Δ(single-nucleotide polymorphism [SNP]-index) method. The result of a QTL linkage analysis with Kompetitive allele-specific PCR (KASP) SNP markers further mapped the GSB resistance locus between the SNP markers KASP_JS9383 and KASP_JS9168 in a region of 571.27 kb on chromosome 8. According to the watermelon gene annotation database, the region contains approximately 19 annotated genes and, of these 19 genes, 2 are disease resistance gene analogs: Cla001017 (coiled-coil nucleotide-binding site leucine-rich repeat resistance protein) and Cla001019 (pathogenesis related). Reverse-transcription quantitative PCR demonstrated that the expression of the two genes changed following S. cucurbitacearum infection, suggesting that they play important roles in GSB resistance in watermelon. This result will facilitate fine mapping and cloning of the Qgsb8.1 locus, and the linked markers will further provide a useful tool for marker-assisted selection of this locus in watermelon breeding programs.
Collapse
Affiliation(s)
- Runsheng Ren
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Jinhua Xu
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Man Zhang
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Guang Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Xiefeng Yao
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Lingli Zhu
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Qian Hou
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| |
Collapse
|
21
|
Melandri G, Sikirou M, Arbelaez JD, Shittu A, Semwal VK, Konaté KA, Maji AT, Ngaujah SA, Akintayo I, Govindaraj V, Shi Y, Agosto-Peréz FJ, Greenberg AJ, Atlin G, Ramaiah V, McCouch SR. Multiple Small-Effect Alleles of Indica Origin Enhance High Iron-Associated Stress Tolerance in Rice Under Field Conditions in West Africa. FRONTIERS IN PLANT SCIENCE 2020; 11:604938. [PMID: 33584748 PMCID: PMC7874229 DOI: 10.3389/fpls.2020.604938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/15/2020] [Indexed: 05/03/2023]
Abstract
Understanding the genetics of field-based tolerance to high iron-associated (HIA) stress in rice can accelerate the development of new varieties with enhanced yield performance in West African lowland ecosystems. To date, few field-based studies have been undertaken to rigorously evaluate rice yield performance under HIA stress conditions. In this study, two NERICA × O. sativa bi-parental rice populations and one O.sativa diversity panel consisting of 296 rice accessions were evaluated for grain yield and leaf bronzing symptoms over multiple years in four West African HIA stress and control sites. Mapping of these traits identified a large number of QTLs and single nucleotide polymorphisms (SNPs) associated with stress tolerance in the field. Favorable alleles associated with tolerance to high levels of iron in anaerobic rice soils were rare and almost exclusively derived from the indica subpopulation, including the most favorable alleles identified in NERICA varieties. These findings highlight the complex genetic architecture underlying rice response to HIA stress and suggest that a recurrent selection program focusing on an expanded indica genepool could be productively used in combination with genomic selection to increase the efficiency of selection in breeding programs designed to enhance tolerance to this prevalent abiotic stress in West Africa.
Collapse
Affiliation(s)
- Giovanni Melandri
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Mouritala Sikirou
- Africa Rice Center, Ibadan, Nigeria
- School of Horticulture and Green Landscaping, Kétou, Bénin
| | - Juan D. Arbelaez
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | | | | | | | | | | | - Inoussa Akintayo
- Central Agricultural Research Institute, Suakoko, Liberia
- Africa Rice Center, Suakoko, Liberia
| | - Vishnu Govindaraj
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Yuxin Shi
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | | | | | - Gary Atlin
- Bill & Melinda Gates Foundation, Seattle, WA, United States
| | | | - Susan R. McCouch
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
- Venuprasad Ramaiah,
| |
Collapse
|
22
|
Sopniewski J, Shams F, Scheele BC, Kefford BJ, Ezaz T. Identifying sex-linked markers in Litoria aurea: a novel approach to understanding sex chromosome evolution in an amphibian. Sci Rep 2019; 9:16591. [PMID: 31719585 PMCID: PMC6851140 DOI: 10.1038/s41598-019-52970-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/25/2019] [Indexed: 01/13/2023] Open
Abstract
Few taxa exhibit the variability of sex-determining modes as amphibians. However, due to the presence of homomorphic sex chromosomes in many species, this phenomenon has been difficult to study. The Australian frog, Litoria aurea, has been relatively well studied over the past 20 years due to widespread declines largely attributable to chytrid fungus. However, it has been subject to few molecular studies and its mode of sex determination remained unknown. We applied DArTseq™ to develop sex-linked single nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 44 phenotypically sexed L. aurea individuals from the Molonglo River in NSW, Australia. We conclusively identified a male heterogametic (XX-XY) sex determination mode in this species, identifying 11 perfectly sex-linked SNP and six strongly sex-linked PA markers. We identified a further 47 moderately sex-linked SNP loci, likely serving as evidence indicative of XY recombination. Furthermore, within these 47 loci, a group of nine males were found to have a feminised Y chromosome that significantly differed to all other males. We postulate ancestral sex-reversal as a means for the evolution of this now pseudoautosomal region on the Y chromosome. Our findings present new evidence for the ‘fountain of youth’ hypothesis for the retention of homomorphic sex chromosomes in amphibians and describe a novel approach for the study of sex chromosome evolution in amphibia.
Collapse
Affiliation(s)
- Jarrod Sopniewski
- Institute for Applied Ecology, University of Canberra, Bruce 2617, Canberra, Australia.
| | - Foyez Shams
- Institute for Applied Ecology, University of Canberra, Bruce 2617, Canberra, Australia
| | - Benjamin C Scheele
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, 2601, Australia
| | - Ben J Kefford
- Institute for Applied Ecology, University of Canberra, Bruce 2617, Canberra, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce 2617, Canberra, Australia.
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Li B, Zhao S, Dou J, Ali A, Gebremeskel H, Gao L, He N, Lu X, Liu W. Genetic mapping and development of molecular markers for a candidate gene locus controlling rind color in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2741-2753. [PMID: 31286160 DOI: 10.1007/s00122-019-03384-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
ClCG08G017810 (ClCGMenG) encoding a 2-phytyl-1,4-beta-naphthoquinone methyltransferase protein is associated with formation of dark green versus light green rind color in watermelon. Rind color is an important agronomic trait in watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai], but the underlying molecular mechanism for this trait is not fully known. In the present study, we identified a single locus on chromosome 8 accounting for watermelon rind color (dark green vs. light green). Genetic analysis of F1, F2, and BC1 populations derived from two parental lines (9904 with dark green rind and Handel with light green rind) revealed that the watermelon rind color (dark green vs. light green) is controlled by a single locus, and dark green is dominant to light green rind. Initial mapping revealed a region of interest spanning 2.07 Mb on chromosome 8. Genetic mapping with CAPS and SNP markers narrowed down the candidate region to 31.4 kb. Gene annotation of the corresponding region in the reference genome revealed the ClCG08G017810 gene sequence encoding the 2-phytyl-1,4-beta-naphthoquinone methyltransferase protein. The sequence alignment of the candidate gene with the two parental lines suggested a nonsynonymous SNP mutation in the coding region of ClCG08G017810, converting an arginine (R) to glycine (G). The SNP might be associated with rind color of 103 watermelon germplasm lines investigated in this study. The qRT-PCR analysis revealed higher expression of ClCG08G017810 in dark green rind than in light green rind. Therefore, ClCG08G017810 is a candidate gene associated with watermelon rind color. The present study facilitates marker-assisted selection useful for the development of cultivars with desirable rind color.
Collapse
Affiliation(s)
- Bingbing Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Junling Dou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Aslam Ali
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Haileslassie Gebremeskel
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Lei Gao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| |
Collapse
|
25
|
Farahani S, Maleki M, Mehrabi R, Kanouni H, Scheben A, Batley J, Talebi R. Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea ( Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers. Genes (Basel) 2019; 10:E676. [PMID: 31487948 PMCID: PMC6770975 DOI: 10.3390/genes10090676] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/26/2019] [Accepted: 08/20/2019] [Indexed: 01/09/2023] Open
Abstract
Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced "Kabuli" breeding lines and Iranian landrace "Desi" chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2 ≥ 0.8, while 2961 pairs of markers showed complete LD (r2 = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.
Collapse
Affiliation(s)
- Somayeh Farahani
- Department of Plant Protection, Varamin-Pishva Branch, Islamic Azad University, Varamin, P.O.Box: 33817-74895, Iran
| | - Mojdeh Maleki
- Department of Plant Protection, Varamin-Pishva Branch, Islamic Azad University, Varamin, P.O.Box: 33817-74895, Iran
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan P.O. Box: 8415683111, Iran
| | - Homayoun Kanouni
- Kordestan Agricultural and Natural Resources and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sanandaj, P.O.Box:714, Iran
| | - Armin Scheben
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Reza Talebi
- Department of Agronomy & Plant Breeding, College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, P.O. Box:618, Iran.
| |
Collapse
|
26
|
Anderson G, Hampton J, Smith N, Rico C. Indications of strong adaptive population genetic structure in albacore tuna ( Thunnus alalunga) in the southwest and central Pacific Ocean. Ecol Evol 2019; 9:10354-10364. [PMID: 31624554 PMCID: PMC6787800 DOI: 10.1002/ece3.5554] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/18/2019] [Accepted: 07/22/2019] [Indexed: 01/09/2023] Open
Abstract
Albacore tuna (Thunnus alalunga) has a distinctly complex life history in which juveniles and adults separate geographically but at times inhabit the same spaces sequentially. The species also migrates long distances and presumably experiences varied regimes of physical stress over a lifetime. There are, therefore, many opportunities for population structure to arise based on stochastic differences or environmental factors that promote local adaptation. However, with the extent of mobility consistently demonstrated by tagged individuals, there is also a strong argument for panmixia within an ocean basin. It is important to confirm such assumptions from a population genetics standpoint for this species in particular because albacore is one of the principal market tuna species that sustains massive global fisheries and yet is also a slow-growing temperate tuna. Consequently, we used 1,837 neutral SNP loci and 89 loci under potential selection to analyze population genetic structure among five sample groups collected from the western and central South Pacific. We found no evidence to challenge panmixia at neutral loci, but strong indications of structuring at adaptive loci. One population sample, from French Polynesia in 2004, was particularly differentiated. Unfortunately, the current study cannot infer whether the divergence is geographic or temporal, or possibly caused by sample distribution. We encourage future studies to include potentially adaptive loci and to continue fine-scale observations within an ocean basin, and not to assume genome-wide panmixia.
Collapse
Affiliation(s)
- Giulia Anderson
- School of Marine StudiesMolecular Analytics Laboratory (MOANA‐LAB)Faculty of Science Technology and EnvironmentThe University of the South PacificSuvaFiji
| | - John Hampton
- Oceanic Fisheries Programme (OFP)Pacific CommunityNouméaNew Caledonia
| | - Neville Smith
- Oceanic Fisheries Programme (OFP)Pacific CommunityNouméaNew Caledonia
| | - Ciro Rico
- School of Marine StudiesMolecular Analytics Laboratory (MOANA‐LAB)Faculty of Science Technology and EnvironmentThe University of the South PacificSuvaFiji
- Instituto de Ciencias Marinas de Andalucía (ICMAN)Consejo Superior de Investigaciones CientíficasCádizSpain
| |
Collapse
|
27
|
Talamantes-Becerra B, Carling J, Kennedy K, Gahan ME, Georges A. Short-read fastA files dataset from complexity-reduced genotyping by sequencing data of bacterial isolates from a public hospital in Australia. Data Brief 2019; 25:104273. [PMID: 31384653 PMCID: PMC6661468 DOI: 10.1016/j.dib.2019.104273] [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: 03/27/2019] [Revised: 07/04/2019] [Accepted: 07/09/2019] [Indexed: 10/27/2022] Open
Abstract
This data article contains short-read sequences (length 30-69 bp) obtained from complexity-reduced genotyping by sequencing (GBS) of 165 samples bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015. These samples represented 14 bacterial species. Data format is shown as filtered fastA files obtained from an Illumina HiSeq2500 sequencer. The experimental factors of this research used three complexity reduction methods with three combinations of restriction enzymes: PstI with MseI, PstI with HpaII and MseI with HpaII.
Collapse
Affiliation(s)
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, Canberra ACT, 2617, Australia
| | - Karina Kennedy
- Canberra Health Services, Departments of Microbiology and Infectious Diseases, Canberra Hospital, Yamba Drive, Garran 2605, Australia
| | - Michelle E Gahan
- National Centre for Forensic Studies, University of Canberra, ACT, 2617, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra ACT 2601, Australia
| |
Collapse
|
28
|
Aguirre-Liguori JA, Gaut BS, Jaramillo-Correa JP, Tenaillon MI, Montes-Hernández S, García-Oliva F, Hearne SJ, Eguiarte LE. Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana). Mol Ecol 2019; 28:2814-2830. [PMID: 30980686 DOI: 10.1111/mec.15098] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 03/27/2019] [Accepted: 04/08/2019] [Indexed: 01/03/2023]
Abstract
Patterns of genomic divergence between hybridizing taxa can be heterogeneous along the genome. Both differential introgression and local adaptation may contribute to this pattern. Here, we analysed two teosinte subspecies, Zea mays ssp. parviglumis and ssp. mexicana, to test whether their divergence has occurred in the face of gene flow and to infer which environmental variables have been important drivers of their ecological differentiation. We generated 9,780 DArTseqTM SNPs for 47 populations, and used an additional data set containing 33,454 MaizeSNP50 SNPs for 49 populations. With these data, we inferred features of demographic history and performed genome wide scans to determine the number of outlier SNPs associated with climate and soil variables. The two data sets indicate that divergence has occurred or been maintained despite continuous gene flow and/or secondary contact. Most of the significant SNP associations were to temperature and to phosphorus concentration in the soil. A large proportion of these candidate SNPs were located in regions of high differentiation that had been identified previously as putative inversions. We therefore propose that genomic differentiation in teosintes has occurred by a process of adaptive divergence, with putative inversions contributing to reduced gene flow between locally adapted populations.
Collapse
Affiliation(s)
- Jonás A Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California
| | - Juan Pablo Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maud I Tenaillon
- Génétique Quantitative et Evolution- Le Moulon, INRA, Gif-sur-Yvette, France
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, México
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, México
| | - Sarah J Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| |
Collapse
|
29
|
Talamantes-Becerra B, Carling J, Kennedy K, Gahan ME, Georges A. Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping. J Microbiol Methods 2019; 160:11-19. [PMID: 30894330 DOI: 10.1016/j.mimet.2019.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/16/2019] [Accepted: 03/17/2019] [Indexed: 11/25/2022]
Abstract
Bacterial identification methods used in routine identification of pathogens in medical microbiology include a combination approach of biochemical tests, mass spectrometry or molecular biology techniques. Extensive publicly-available databases of DNA sequence data from pathogenic bacteria have been amassed in recent years; this provides an opportunity for using bacterial genome sequencing for identification purposes. Whole genome sequencing is increasing in popularity, although at present it remains a relatively expensive approach to bacterial identification and typing. Complexity-reduced bacterial genome sequencing provides an alternative. We evaluate genomic complexity-reduction using restriction enzymes and sequencing to identify bacterial isolates. A total of 165 bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015 were used in this study. They were identified and typed by the Microbiology Department of Canberra Public Hospital, and represented 14 bacterial species. DNA extractions from these samples were processed using a combination of the restriction enzymes PstI with MseI, PstI with HpaII and MseI with HpaII. The resulting sequences (length 30-69 bp) were aligned against publicly available bacterial genome and plasmid sequences. Results of the alignment were processed using a bioinformatics pipeline developed for this project, Currito3.1 DNA Fragment Analysis Software. All 165 samples were correctly identified to genus and species by each of the three combinations of restriction enzymes. A further 35 samples typed to the level of strain identified and compared for consistency with MLST typing data and in silico MLST data derived from the nearest sequenced candidate reference. The high level of agreement between bacterial identification using complexity-reduced genome sequencing and standard hospital identifications indicating that this new approach is a viable alternative for identification of bacterial isolates derived from pathology specimens. The effectiveness of species identification and in particular, strain typing, depends on access to a comprehensive and taxonomically accurate bacterial genome sequence database containing relevant bacterial species and strains.
Collapse
Affiliation(s)
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, Canberra, ACT 2617, Australia
| | - Karina Kennedy
- Canberra Health Services, Departments of Microbiology and Infectious Diseases, Canberra Hospital, Yamba Drive, Garran 2605, Australia
| | - Michelle E Gahan
- National Centre for Forensic Studies, University of Canberra, ACT, 2617, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, ACT 2601, Australia
| |
Collapse
|
30
|
Li B, Lu X, Dou J, Aslam A, Gao L, Zhao S, He N, Liu W. Construction of A High-Density Genetic Map and Mapping of Fruit Traits in Watermelon ( Citrullus Lanatus L.) Based on Whole-Genome Resequencing. Int J Mol Sci 2018; 19:ijms19103268. [PMID: 30347873 PMCID: PMC6214002 DOI: 10.3390/ijms19103268] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 12/26/2022] Open
Abstract
Watermelon (Citrullus lanatus L.) is an important horticultural crop that is grown worldwide and has a high economic value. To dissect the loci associated with important horticultural traits and to analyze the genetic and genomic information of this species, a high-density genetic map was constructed based on whole-genome resequencing (WGR), a powerful high-resolution method for single-nucleotide polymorphism (SNP) marker development, genetic map construction, and gene mapping. Resequencing of both parental lines and 126 recombinant inbred lines (RIL) resulted in the detection of 178,762 single-nucleotide polymorphism (SNP) markers in the parental lines at a sequencing depth greater than four-fold. Additionally, 2132 recombination bin markers comprising 103,029 SNP markers were mapped onto 11 linkage groups (LGs). Substantially more SNP markers were mapped to the genetic map compared with other recent studies. The total length of the linkage map was 1508.94 cM, with an average distance of 0.74 cM between adjacent bin markers. Based on this genetic map, one locus for fruit bitterness, one locus for rind color, and one locus for seed coat color with high LOD scores (58.361, 18.353, 26.852) were identified on chromosome 1, chromosome 8, and chromosome 3, respectively. These prominent loci were identified in a region of 6.16 Mb, 2.07 Mb, and 0.37 Mb, respectively. On the basis of current research, the high-density map and mapping results will provide a valuable tool for identifying candidate genes, map-based gene cloning, comparative mapping, and marker-assisted selection (MAS) in watermelon breeding.
Collapse
Affiliation(s)
- Bingbing Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Junling Dou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Ali Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Lei Gao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| |
Collapse
|
31
|
Naresh P, Lin SW, Lin CY, Wang YW, Schafleitner R, Kilian A, Kumar S. Molecular Markers Associated to Two Non-allelic Genic Male Sterility Genes in Peppers ( Capsicum annuum L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1343. [PMID: 30386350 PMCID: PMC6198792 DOI: 10.3389/fpls.2018.01343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
Male sterility is of high importance in hybrid seed production of hot and sweet peppers. Genic (or nuclear) male sterility (GMS) is a simply inherited (usually monogenic recessive) and highly stable trait. However, one major disadvantage of using GMS is 1:1 segregation of male sterile to male fertile plants in every subsequent generation. Molecular markers tightly linked to genic male sterility (ms) genes would facilitate an efficient and rapid transfer of ms genes into different genetic backgrounds through marker-assisted backcrossing. The two non-allelic genic male sterility genes ms3 and ms w in hot and sweet pepper backgrounds, respectively, are monogenic recessive. Genotyping by sequencing (GBS) in an F2 population segregating for ms3 gene in hot pepper and in an F6 inbred near-isogenic line (NIL) population segregating for ms w gene in sweet pepper yielded 9,713 and 7,453 single nucleotide polymorphism markers, respectively. Four candidate SNPs co-segregating with ms3 gene and one co-segregating with ms w gene were identified by bulk segregant analysis and physically mapped to chromosomes 1 and 5, respectively. In hot pepper, two markers [HPGMS2 (CAPS) and HPGMS3 (dCAPS)] located 3.83 cM away from the ms3 gene and in sweet pepper the dCAPS marker SPGMS1 co-segregated (completely linked) with the ms w gene were developed. These markers will increase the efficacy of the male sterility genes for pepper breeding, as they can be useful in developing the genic male sterile lines in parental inbred lines of commercial hybrids through marker-assisted backcrossing, hybrid seed production, and genetic purity testing of hybrid seeds.
Collapse
Affiliation(s)
- Ponnam Naresh
- Central Horticultural Experiment Station, ICAR-Indian Institute of Horticultural Research, Bhubaneswar, India
| | - Shih-wen Lin
- World Vegetable Center (WorldVeg), Tainan, Taiwan
| | - Chen-yu Lin
- World Vegetable Center (WorldVeg), Tainan, Taiwan
| | - Yen-wei Wang
- World Vegetable Center (WorldVeg), Tainan, Taiwan
| | | | | | | |
Collapse
|
32
|
Hill PL, Burridge CP, Ezaz T, Wapstra E. Conservation of Sex-Linked Markers among Conspecific Populations of a Viviparous Skink, Niveoscincus ocellatus, Exhibiting Genetic and Temperature-Dependent Sex Determination. Genome Biol Evol 2018; 10:1079-1087. [PMID: 29659810 PMCID: PMC5905450 DOI: 10.1093/gbe/evy042] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2018] [Indexed: 12/18/2022] Open
Abstract
Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here, we tested for differences in sex-linked markers in the only known reptile that is polymorphic for sex determination system, the spotted snow skink, Niveoscincus ocellatus, to quantify the genomic differences that have accompanied this transition. In a highland population, sex is determined genetically, whereas in a lowland population, offspring sex ratio is influenced by temperature. We found a similar number of sex-linked loci in each population, including shared loci, with genotypes consistent with male heterogamety (XY). However, population-specific linkage disequilibrium suggests greater differentiation of sex chromosomes in the highland population. Our results suggest that transitions between sex determination systems can be facilitated by subtle genetic differences.
Collapse
Affiliation(s)
- Peta L Hill
- School of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania, Australia
| | | | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Erik Wapstra
- School of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania, Australia
| |
Collapse
|
33
|
Borzęcka E, Hawliczek-Strulak A, Bolibok L, Gawroński P, Tofil K, Milczarski P, Stojałowski S, Myśków B, Targońska-Karasek M, Grądzielewska A, Smolik M, Kilian A, Bolibok-Brągoszewska H. Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye. Sci Rep 2018; 8:8428. [PMID: 29849048 PMCID: PMC5976670 DOI: 10.1038/s41598-018-26541-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/16/2018] [Indexed: 11/09/2022] Open
Abstract
Identification of bacterial artificial chromosome (BAC) clones containing specific sequences is a prerequisite for many applications, such as physical map anchoring or gene cloning. Existing BAC library screening strategies are either low-throughput or require a considerable initial input of resources for platform establishment. We describe a high-throughput, reliable, and cost-effective BAC library screening approach deploying genotyping platforms which are independent from the availability of sequence information: a genotyping-by-sequencing (GBS) method DArTSeq and the microarray-based Diversity Arrays Technology (DArT). The performance of these methods was tested in a very large and complex rye genome. The DArTseq approach delivered superior results: a several fold higher efficiency of addressing genetic markers to BAC clones and anchoring of BAC clones to genetic map and also a higher reliability. Considering the sequence independence of the platform, the DArTseq-based library screening can be proposed as an attractive method to speed up genomics research in resource poor species.
Collapse
Affiliation(s)
- Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Anna Hawliczek-Strulak
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Leszek Bolibok
- Department of Silviculture, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Paweł Milczarski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Stefan Stojałowski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Małgorzata Targońska-Karasek
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Agnieszka Grądzielewska
- Institute of Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
| | - Miłosz Smolik
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Kirinari st, ACT 2617, Bruce, Australia
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland.
| |
Collapse
|
34
|
Tyrka M, Oleszczuk S, Rabiza-Swider J, Wos H, Wedzony M, Zimny J, Ponitka A, Ślusarkiewicz-Jarzina A, Metzger RJ, Baenziger PS, Lukaszewski AJ. Populations of doubled haploids for genetic mapping in hexaploid winter triticale. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:46. [PMID: 29623004 PMCID: PMC5878199 DOI: 10.1007/s11032-018-0804-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
To create a framework for genetic dissection of hexaploid triticale, six populations of doubled haploid (DH) lines were developed from pairwise hybrids of high-yielding winter triticale cultivars. The six populations comprise between 97 and 231 genotyped DH lines each, totaling 957 DH lines. A consensus genetic map spans 4593.9 cM is composed of 1576 unique DArT markers. The maps reveal several structural rearrangements in triticale genomes. In preliminary tests of the populations and maps, markers specific to wheat segments of the engineered rye chromosome 1R (RM1B) were identified. Example QTL mapping of days to heading in cv. Krakowiak revealed loci on chromosomes 2BL and 2R responsible for extended vernalization requirement, and candidate genes were identified. The material is available to all parties interested in triticale genetics.
Collapse
Affiliation(s)
- M. Tyrka
- Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Rzeszow, Poland
| | - S. Oleszczuk
- Institute of Plant Breeding and Acclimatization, National Research Institute, Radzikow, Poland
| | - J. Rabiza-Swider
- Department of Ornamental Plants, Warsaw University of Life Sciences, Warsaw, Poland
| | - H. Wos
- Plant Breeding Strzelce Ltd., Co. - IHAR-PIB Group, Strzelce, Poland
| | - M. Wedzony
- Department of Cell Biology and Genetics, Pedagogical University of Cracow, Kraków, Poland
| | - J. Zimny
- Institute of Plant Breeding and Acclimatization, National Research Institute, Radzikow, Poland
| | - A. Ponitka
- Institute of Plant Genetics, Poznan, Poland
| | | | - R. J. Metzger
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-3002 USA
| | - P. S. Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE USA
| | - A. J. Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| |
Collapse
|
35
|
Genome-wide comparisons reveal evidence for a species complex in the black-lip pearl oyster Pinctada margaritifera (Bivalvia: Pteriidae). Sci Rep 2018; 8:191. [PMID: 29317743 PMCID: PMC5760631 DOI: 10.1038/s41598-017-18602-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 12/14/2017] [Indexed: 02/05/2023] Open
Abstract
Evolutionary relationships in the black-lip pearl oyster Pinctada margaritifera which is highly valued for pearl production remain poorly understood. This species possesses an 18,000 km Indo-Pacific natural distribution, and its current description includes six subspecies defined exclusively on morphological characters. To evaluate its taxonomic identity using molecular data, 14 populations in both the Indian and Pacific Oceans (n = 69), and the congeneric taxa P. maxima and P. mazatlanica (n = 29 and n = 10, respectively) were sampled. Phylogenomic reconstruction was carried out using both 8,308 genome-wide SNPs and 10,000 dominant loci (DArTseq PAVs). Reconstructions using neighbour-joining (Nei's 1972 distances), maximum likelihood and Bayesian approaches all indicate that the taxonomy of P. margaritifera is quite complex, with distinct evolutionary significant units (ESUs) identified within Tanzanian and Iranian populations. Contrastingly, phylogenies generated for Pacific Ocean oysters resolved a large monophyletic clade, suggesting little support for two current morphological subspecies classifications. Furthermore, P. mazatlanica formed a basal clade closest to French Polynesian P. margaritifera, suggesting it may be conspecific. Collectively, these findings provide evidence that P. margaritifera comprises a species complex, perhaps as a result of population fragmentation and increased divergence at range limits.
Collapse
|
36
|
Barilli E, Cobos MJ, Carrillo E, Kilian A, Carling J, Rubiales D. A High-Density Integrated DArTseq SNP-Based Genetic Map of Pisum fulvum and Identification of QTLs Controlling Rust Resistance. FRONTIERS IN PLANT SCIENCE 2018; 9:167. [PMID: 29497430 PMCID: PMC5818415 DOI: 10.3389/fpls.2018.00167] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/30/2018] [Indexed: 05/05/2023]
Abstract
Pisum fulvum, a wild relative of pea is an important source of allelic diversity to improve the genetic resistance of cultivated species against fungal diseases of economic importance like the pea rust caused by Uromyces pisi. To unravel the genetic control underlying resistance to this fungal disease, a recombinant inbred line (RIL) population was generated from a cross between two P. fulvum accessions, IFPI3260 and IFPI3251, and genotyped using Diversity Arrays Technology. A total of 9,569 high-quality DArT-Seq and 8,514 SNPs markers were generated. Finally, a total of 12,058 markers were assembled into seven linkage groups, equivalent to the number of haploid chromosomes of P. fulvum and P. sativum. The newly constructed integrated genetic linkage map of P. fulvum covered an accumulated distance of 1,877.45 cM, an average density of 1.19 markers cM-1 and an average distance between adjacent markers of 1.85 cM. The composite interval mapping revealed three QTLs distributed over two linkage groups that were associated with the percentage of rust disease severity (DS%). QTLs UpDSII and UpDSIV were located in the LGs II and IV respectively and were consistently identified both in adult plants over 3 years at the field (Córdoba, Spain) and in seedling plants under controlled conditions. Whenever they were detected, their contribution to the total phenotypic variance varied between 19.8 and 29.2. A third QTL (UpDSIV.2) was also located in the LGIVand was environmentally specific as was only detected for DS % in seedlings under controlled conditions. It accounted more than 14% of the phenotypic variation studied. Taking together the data obtained in the study, it could be concluded that the expression of resistance to fungal diseases in P. fulvum originates from the resistant parent IFPI3260.
Collapse
Affiliation(s)
| | - María J Cobos
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | | | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Canberra, ACT, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, University of Canberra, Canberra, ACT, Australia
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| |
Collapse
|
37
|
Ndjiondjop MN, Semagn K, Sow M, Manneh B, Gouda AC, Kpeki SB, Pegalepo E, Wambugu P, Sié M, Warburton ML. Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs. FRONTIERS IN PLANT SCIENCE 2018; 9:446. [PMID: 29686690 PMCID: PMC5900792 DOI: 10.3389/fpls.2018.00446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 03/22/2018] [Indexed: 05/04/2023]
Abstract
Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several 'New Rice for Africa (NERICA)' improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as 'Advanced Rice for Africa (ARICA)'. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs). A sample of 11 ARICAs, 85 NERICAs, 62 O. sativa spp. japonica, and 172 O. sativa spp. indica genotypes were genotyped with 27,560 SNPs using diversity array technology (DArT)-based sequencing (DArTseq) platform. Nearly 66% of the SNPs were polymorphic, of which 15,020 SNPs were mapped to the 12 rice chromosomes. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA, and NERICA varied from 0.016 to 0.623, from 0.020 to 0.692, from 0.075 to 0.763, and from 0.014 to 0.644, respectively. The proportion of pairs of genotypes with genetic distance > 0.400 was the largest within NERICAs (35.1% of the pairs) followed by ARICAs (18.2%), japonica (17.4%), and indica (5.6%). We found one pair of japonica, 11 pairs of indica, and 35 pairs of NERICA genotypes differing by <2% of the total scored alleles, which was due to 26 pairs of genotypes with identical pedigrees. Cluster analysis, principal component analysis, and the model-based population structure analysis all revealed two distinct groups corresponding to the lowland (primarily indica and lowland NERICAs) and upland (japonica and upland NERICAs) growing ecologies. Most of the interspecific lowland NERICAs formed a sub-group, likely caused by differences in the O. glaberrima genome as compared with the indica genotypes. Analysis of molecular variance revealed very great genetic differentiation (FST = 0.688) between the lowland and upland ecologies, and 31.2% of variation attributable to differences within cluster groups. About 8% (1,197 of 15,020) of the 15,020 SNPs were significantly (P < 0.05) different between the lowland and upland ecologies and formed contrasting haplotypes that could clearly discriminate lowland from upland genotypes. This is the first study using high density markers that characterized NERICA and ARICA varieties in comparison with indica and japonica varieties widely used in Africa, which could aid rice breeders on parent selection for developing new improved rice germplasm.
Collapse
Affiliation(s)
- Marie Noelle Ndjiondjop
- Africa Rice Center (AfricaRice), Bouaké, Côte d’Ivoire
- *Correspondence: Marie Noelle Ndjiondjop, Kassa Semagn,
| | - Kassa Semagn
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Marie Noelle Ndjiondjop, Kassa Semagn,
| | | | | | | | | | | | - Peterson Wambugu
- Genetic Resources Research Institute, Kenya Agricultural & Livestock Research Organization, Nairobi, Kenya
| | | | - Marilyn L. Warburton
- Corn Host Plant Resistance Research Unit, United States Department of Agriculture-Agricultural Research Service, Starkville, MS, United States
| |
Collapse
|
38
|
High density SNP and DArT-based genetic linkage maps of two closely related oil palm populations. J Appl Genet 2017; 59:23-34. [PMID: 29214520 DOI: 10.1007/s13353-017-0420-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/16/2017] [Accepted: 11/23/2017] [Indexed: 12/22/2022]
Abstract
Oil palm (Elaeis guineensis Jacq.) is an outbreeding perennial tree crop with long breeding cycles, typically 12 years. Molecular marker technologies can greatly improve the breeding efficiency of oil palm. This study reports the first use of the DArTseq platform to genotype two closely related self-pollinated oil palm populations, namely AA0768 and AA0769 with 48 and 58 progeny respectively. Genetic maps were constructed using the DArT and SNP markers generated in combination with anchor SSR markers. Both maps consisted of 16 major independent linkage groups (2n = 2× = 32) with 1399 and 1466 mapped markers for the AA0768 and AA0769 populations, respectively, including the morphological trait "shell-thickness" (Sh). The map lengths were 1873.7 and 1720.6 cM with an average marker density of 1.34 and 1.17 cM, respectively. The integrated map was 1803.1 cM long with 2066 mapped markers and average marker density of 0.87 cM. A total of 82% of the DArTseq marker sequence tags identified a single site in the published genome sequence, suggesting preferential targeting of gene-rich regions by DArTseq markers. Map integration of higher density focused around the Sh region identified closely linked markers to the Sh, with D.15322 marker 0.24 cM away from the morphological trait and 5071 bp from the transcriptional start of the published SHELL gene. Identification of the Sh marker demonstrates the robustness of using the DArTseq platform to generate high density genetic maps of oil palm with good genome coverage. Both genetic maps and integrated maps will be useful for quantitative trait loci analysis of important yield traits as well as potentially assisting the anchoring of genetic maps to genomic sequences.
Collapse
|
39
|
Valdisser PAMR, Pereira WJ, Almeida Filho JE, Müller BSF, Coelho GRC, de Menezes IPP, Vianna JPG, Zucchi MI, Lanna AC, Coelho ASG, de Oliveira JP, Moraes ADC, Brondani C, Vianello RP. In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping. BMC Genomics 2017; 18:423. [PMID: 28558696 PMCID: PMC5450071 DOI: 10.1186/s12864-017-3805-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/17/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. RESULTS Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp. CONCLUSIONS For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.
Collapse
Affiliation(s)
- Paula A. M. R. Valdisser
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Wendell J. Pereira
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasília, DF Brazil
| | - Jâneo E. Almeida Filho
- Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, RJ Brazil
| | - Bárbara S. F. Müller
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasília, DF Brazil
| | | | - Ivandilson P. P. de Menezes
- Laboratório de Genética e Biologia Molecular, Departamento de Biologia, Instituto Federal Goiano (IF Goiano), Urutaí, GO Brazil
| | - João P. G. Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Maria I. Zucchi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Anna C. Lanna
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
| | | | | | | | - Claudio Brondani
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
| | - Rosana P. Vianello
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
| |
Collapse
|
40
|
Steane DA, Mclean EH, Potts BM, Prober SM, Stock WD, Stylianou VM, Vaillancourt RE, Byrne M. Evidence for adaptation and acclimation in a widespread eucalypt of semi-arid Australia. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw051] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Dorothy A. Steane
- School of Biological Sciences and ARC Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, 4556, Australia
- CSIRO Land and Water, Private Bag 5, Wembley 6913, Western Australia
| | - Elizabeth H. Mclean
- CSIRO Land and Water, Private Bag 5, Wembley 6913, Western Australia
- Science and Conservation Division, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia
| | - Brad M. Potts
- School of Biological Sciences and ARC Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Suzanne M. Prober
- CSIRO Land and Water, Private Bag 5, Wembley 6913, Western Australia
| | - William D. Stock
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, 6027, Western Australia
| | - Vanessa M. Stylianou
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, 6027, Western Australia
| | - René E. Vaillancourt
- School of Biological Sciences and ARC Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia
| |
Collapse
|
41
|
Padmanaban S, Zhang P, Hare RA, Sutherland MW, Martin A. Pentaploid Wheat Hybrids: Applications, Characterisation, and Challenges. FRONTIERS IN PLANT SCIENCE 2017; 8:358. [PMID: 28367153 PMCID: PMC5355473 DOI: 10.3389/fpls.2017.00358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/01/2017] [Indexed: 05/09/2023]
Abstract
Interspecific hybridisation between hexaploid and tetraploid wheat species leads to the development of F1 pentaploid hybrids with unique chromosomal constitutions. Pentaploid hybrids derived from bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum spp. durum Desf.) crosses can improve the genetic background of either parent by transferring traits of interest. The genetic variability derived from bread and durum wheat and transferred into pentaploid hybrids has the potential to improve disease resistance, abiotic tolerance, and grain quality, and to enhance agronomic characters. Nonetheless, pentaploid wheat hybrids have not been fully exploited in breeding programs aimed at improving crops. There are several potential barriers for efficient pentaploid wheat production, such as low pollen compatibility, poor seed set, failed seedling establishment, and frequent sterility in F1 hybrids. However, most of the barriers can be overcome by careful selection of the parental genotypes and by employing the higher ploidy level genotype as the maternal parent. In this review, we summarize the current research on pentaploid wheat hybrids and analyze the advantages and pitfalls of current methods used to assess pentaploid-derived lines. Furthermore, we discuss current and potential applications in commercial breeding programs and future directions for research into pentaploid wheat.
Collapse
Affiliation(s)
- Sriram Padmanaban
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Peng Zhang
- Plant Breeding Institute, The University of Sydney, SydneyNSW, Australia
| | - Ray A. Hare
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Mark W. Sutherland
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| |
Collapse
|
42
|
Lal MM, Southgate PC, Jerry DR, Bosserelle C, Zenger KR. Swept away: ocean currents and seascape features influence genetic structure across the 18,000 Km Indo-Pacific distribution of a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera. BMC Genomics 2017; 18:66. [PMID: 28073363 PMCID: PMC5225542 DOI: 10.1186/s12864-016-3410-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic structure in many widely-distributed broadcast spawning marine invertebrates remains poorly understood, posing substantial challenges for their fishery management, conservation and aquaculture. Under the Core-Periphery Hypothesis (CPH), genetic diversity is expected to be highest at the centre of a species' distribution, progressively decreasing with increased differentiation towards outer range limits, as populations become increasingly isolated, fragmented and locally adapted. The unique life history characteristics of many marine invertebrates such as high dispersal rates, stochastic survival and variable recruitment are also likely to influence how populations are organised. To examine the microevolutionary forces influencing population structure, connectivity and adaptive variation in a highly-dispersive bivalve, populations of the black-lip pearl oyster Pinctada margaritifera were examined across its ~18,000 km Indo-Pacific distribution. RESULTS Analyses utilising 9,624 genome-wide SNPs and 580 oysters, discovered differing patterns of significant and substantial broad-scale genetic structure between the Indian and Pacific Ocean basins. Indian Ocean populations were markedly divergent (F st = 0.2534-0.4177, p < 0.001), compared to Pacific Ocean oysters, where basin-wide gene flow was much higher (F st = 0.0007-0.1090, p < 0.001). Partitioning of genetic diversity (hierarchical AMOVA) attributed 18.1% of variance between ocean basins, whereas greater proportions were resolved within samples and populations (45.8% and 35.7% respectively). Visualisation of population structure at selectively neutral loci resolved three and five discrete genetic clusters for the Indian and Pacific Oceans respectively. Evaluation of genetic structure at adaptive loci for Pacific populations (89 SNPs under directional selection; F st = 0.1012-0.4371, FDR = 0.05), revealed five clusters identical to those detected at neutral SNPs, suggesting environmental heterogeneity within the Pacific. Patterns of structure and connectivity were supported by Mantel tests of isolation by distance (IBD) and independent hydrodynamic particle dispersal simulations. CONCLUSIONS It is evident that genetic structure and connectivity across the natural range of P. margaritifera is highly complex, and produced by the interaction of ocean currents, IBD and seascape features at a broad scale, together with habitat geomorphology and local adaptation at regional levels. Overall population organisation is far more elaborate than generalised CPH predictions, however valuable insights for regional fishery management, and a greater understanding of range-wide genetic structure in a highly-dispersive marine invertebrate have been gained.
Collapse
Affiliation(s)
- Monal M. Lal
- Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811 QLD Australia
| | - Paul C. Southgate
- Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811 QLD Australia
- Australian Centre for Pacific Islands Research, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558 QLD Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811 QLD Australia
| | - Cyprien Bosserelle
- Geoscience Division, Secretariat of the Pacific Community, 241 Mead Road, Nabua, Suva Fiji Islands
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811 QLD Australia
| |
Collapse
|
43
|
Ndjiondjop MN, Semagn K, Gouda AC, Kpeki SB, Dro Tia D, Sow M, Goungoulou A, Sie M, Perrier X, Ghesquiere A, Warburton ML. Genetic Variation and Population Structure of Oryza glaberrima and Development of a Mini-Core Collection Using DArTseq. FRONTIERS IN PLANT SCIENCE 2017; 8:1748. [PMID: 29093721 PMCID: PMC5651524 DOI: 10.3389/fpls.2017.01748] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/25/2017] [Indexed: 05/20/2023]
Abstract
The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97-99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1-89.2% attributable to differences within groups.
Collapse
Affiliation(s)
- Marie-Noelle Ndjiondjop
- Africa Rice Center (AfricaRice), Bouake, Cote d'Ivoire
- *Correspondence: Marie-Noelle Ndjiondjop
| | - Kassa Semagn
- Department of Agriculture, Forestry and Nutrition Science, University of Alberta, Edmonton, Canada
| | | | | | | | - Mounirou Sow
- Africa Rice Center (AfricaRice), Ibadan, Nigeria
| | | | - Moussa Sie
- Africa Rice Center (AfricaRice), Centre National de la Recherche Appliquée au Développement Rural (FOFIFA), Antananarivo, Madagascar
| | - Xavier Perrier
- Unité Mixte de Recherche Amélioration Génétique, CIRAD, Montpellier, France
- University of Montpellier, Montpellier, France
| | - Alain Ghesquiere
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Marilyn L. Warburton
- Corn Host Plant Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Starkville, Mississippi, United States
| |
Collapse
|
44
|
Garavito A, Montagnon C, Guyot R, Bertrand B. Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico. BMC PLANT BIOLOGY 2016; 16:242. [PMID: 27814672 PMCID: PMC5096298 DOI: 10.1186/s12870-016-0933-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/25/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND The coffee species Coffea canephora is commercially identified as "Conilon" when produced in Brazil, or "Robusta" when produced elsewhere in the world. It represents approximately 40 % of coffee production worldwide. While the genetic diversity of wild C. canephora has been well studied in the past, only few studies have addressed the genetic diversity of currently cultivated varieties around the globe. Vietnam is the largest Robusta producer in the world, while Mexico is the only Latin American country, besides Brazil, that has a significant Robusta production. Knowledge of the genetic origin of Robusta cultivated varieties in countries as important as Vietnam and Mexico is therefore of high interest. RESULTS Through the use of Sequencing-based diversity array technology-DArTseq method-on a collection of C. canephora composed of known accessions and accessions cultivated in Vietnam and Mexico, 4,021 polymorphic SNPs were identified. We used a multivariate analysis using SNP data from reference accessions in order to confirm and further fine-tune the genetic diversity of C. canephora. Also, by interpolating the data obtained for the varieties from Vietnam and Mexico, we determined that they are closely related to each other, and identified that their genetic origin is the Robusta Congo - Uganda group. CONCLUSIONS The genetic characterization based on SNP markers of the varieties grown throughout the world, increased our knowledge on the genetic diversity of C. canephora, and contributed to the understanding of the genetic background of varieties from very important coffee producers. Given the common genetic origin of the Robusta varieties cultivated in Vietnam, Mexico and Uganda, and the similar characteristics of climatic areas and relatively high altitude where they are grown, we can state that the Vietnamese and the Mexican Robusta have the same genetic potential to produce good cup quality.
Collapse
Affiliation(s)
- Andrea Garavito
- Present Address: Centro de Bioinformática y biología computacional de Colombia – BIOS, Ecoparque los Yarumos, Manizales, Caldas Colombia
| | | | - Romain Guyot
- CIRAD, IRD, Interactions plants - micro-organisms - environment (IPME), Montpellier University, 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | - Benoît Bertrand
- CIRAD, IRD, Interactions plants - micro-organisms - environment (IPME), Montpellier University, 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| |
Collapse
|
45
|
Chen J, Zavala C, Ortega N, Petroli C, Franco J, Burgueño J, Costich DE, Hearne SJ. The Development of Quality Control Genotyping Approaches: A Case Study Using Elite Maize Lines. PLoS One 2016; 11:e0157236. [PMID: 27280295 PMCID: PMC4900658 DOI: 10.1371/journal.pone.0157236] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 05/26/2016] [Indexed: 02/07/2023] Open
Abstract
Quality control (QC) of germplasm identity and purity is a critical component of breeding and conservation activities. SNP genotyping technologies and increased availability of markers provide the opportunity to employ genotyping as a low-cost and robust component of this QC. In the public sector available low-cost SNP QC genotyping methods have been developed from a very limited panel of markers of 1,000 to 1,500 markers without broad selection of the most informative SNPs. Selection of optimal SNPs and definition of appropriate germplasm sampling in addition to platform section impact on logistical and resource-use considerations for breeding and conservation applications when mainstreaming QC. In order to address these issues, we evaluated the selection and use of SNPs for QC applications from large DArTSeq data sets generated from CIMMYT maize inbred lines (CMLs). Two QC genotyping strategies were developed, the first is a “rapid QC”, employing a small number of SNPs to identify potential mislabeling of seed packages or plots, the second is a “broad QC”, employing a larger number of SNP, used to identify each germplasm entry and to measure heterogeneity. The optimal marker selection strategies combined the selection of markers with high minor allele frequency, sampling of clustered SNP in proportion to marker cluster distance and selecting markers that maintain a uniform genomic distribution. The rapid and broad QC SNP panels selected using this approach were further validated using blind test assessments of related re-generation samples. The influence of sampling within each line was evaluated. Sampling 192 individuals would result in close to 100% possibility of detecting a 5% contamination in the entry, and approximately a 98% probability to detect a 2% contamination of the line. These results provide a framework for the establishment of QC genotyping. A comparison of financial and time costs for use of these approaches across different platforms is discussed providing a framework for institutions involved in maize conservation and breeding to assess the resource use effectiveness of QC genotyping. Application of these research findings, in combination with existing QC approaches, will ensure the regeneration, distribution and use in breeding of true to type inbred germplasm. These findings also provide an effective approach to optimize SNP selection for QC genotyping in other species.
Collapse
Affiliation(s)
- Jiafa Chen
- International Maize and Wheat Improvement Center (CIMMYT); Texcoco; Edo. De Mexico; Mexico CP 56237
| | - Cristian Zavala
- International Maize and Wheat Improvement Center (CIMMYT); Texcoco; Edo. De Mexico; Mexico CP 56237
| | - Noemi Ortega
- International Maize and Wheat Improvement Center (CIMMYT); Texcoco; Edo. De Mexico; Mexico CP 56237
| | - Cesar Petroli
- International Maize and Wheat Improvement Center (CIMMYT); Texcoco; Edo. De Mexico; Mexico CP 56237
| | - Jorge Franco
- International Maize and Wheat Improvement Center (CIMMYT); Texcoco; Edo. De Mexico; Mexico CP 56237
- Departamento de Biometría, Universidad de la Republica, Paysandú; Uruguay CP 60000
| | - Juan Burgueño
- International Maize and Wheat Improvement Center (CIMMYT); Texcoco; Edo. De Mexico; Mexico CP 56237
| | - Denise E. Costich
- International Maize and Wheat Improvement Center (CIMMYT); Texcoco; Edo. De Mexico; Mexico CP 56237
- * E-mail: (DEC); (SJH)
| | - Sarah J. Hearne
- International Maize and Wheat Improvement Center (CIMMYT); Texcoco; Edo. De Mexico; Mexico CP 56237
- * E-mail: (DEC); (SJH)
| |
Collapse
|
46
|
Milczarski P, Hanek M, Tyrka M, Stojałowski S. The application of GBS markers for extending the dense genetic map of rye (Secale cereale L.) and the localization of the Rfc1 gene restoring male fertility in plants with the C source of sterility-inducing cytoplasm. J Appl Genet 2016; 57:439-451. [PMID: 27085345 PMCID: PMC5061839 DOI: 10.1007/s13353-016-0347-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/22/2016] [Accepted: 03/27/2016] [Indexed: 11/28/2022]
Abstract
Genotyping by sequencing (GBS) is an efficient method of genotyping in numerous plant species. One of the crucial steps toward the application of GBS markers in crop improvement is anchoring them on particular chromosomes. In rye (Secale cereale L.), chromosomal localization of GBS markers has not yet been reported. In this paper, the application of GBS markers generated by the DArTseq platform for extending the high-density map of rye is presented. Additionally, their application is used for the localization of the Rfc1 gene that restores male fertility in plants with the C source of sterility-inducing cytoplasm. The total number of markers anchored on the current version of the map is 19,081, of which 18,132 were obtained from the DArTseq platform. Numerous markers co-segregated within the studied mapping population, so, finally, only 3397 unique positions were located on the map of all seven rye chromosomes. The total length of the map is 1593 cM and the average distance between markers is 0.47 cM. In spite of the resolution of the map being not very high, it should be a useful tool for further studies of the Secale cereale genome because of the presence on this map of numerous GBS markers anchored for the first time on rye chromosomes. The Rfc1 gene was located on high-density maps of the long arm of the 4R chromosome obtained for two mapping populations. Genetic maps were composed of DArT, DArTseq, and PCR-based markers. Consistent mapping results were obtained and DArTs tightly linked to the Rfc1 gene were successfully applied for the development of six new PCR-based markers useful in marker-assisted selection.
Collapse
Affiliation(s)
- Paweł Milczarski
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434, Szczecin, Poland
| | - Monika Hanek
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434, Szczecin, Poland
| | - Mirosław Tyrka
- Department of Biochemistry and Biotechnology, Rzeszów University of Technology, Powstańców Warszawy 6, 35-959, Rzeszów, Poland
| | - Stefan Stojałowski
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434, Szczecin, Poland.
| |
Collapse
|
47
|
Zhou Z, Zhang C, Zhou Y, Hao Z, Wang Z, Zeng X, Di H, Li M, Zhang D, Yong H, Zhang S, Weng J, Li X. Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines. BMC Genomics 2016; 17:178. [PMID: 26940065 PMCID: PMC4778306 DOI: 10.1186/s12864-016-2555-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/29/2016] [Indexed: 11/21/2022] Open
Abstract
Background Plant architecture attributes, such as plant height, ear height, and internode number, have played an important role in the historical increases in grain yield, lodging resistance, and biomass in maize (Zea mays L.). Analyzing the genetic basis of variation in plant architecture using high density QTL mapping will be of benefit for the breeding of maize for many traits. However, the low density of molecular markers in existing genetic maps has limited the efficiency and accuracy of QTL mapping. Genotyping by sequencing (GBS) is an improved strategy for addressing a complex genome via next-generation sequencing technology. GBS has been a powerful tool for SNP discovery and high-density genetic map construction. The creation of ultra-high density genetic maps using large populations of advanced recombinant inbred lines (RILs) is an efficient way to identify QTL for complex agronomic traits. Results A set of 314 RILs derived from inbreds Ye478 and Qi319 were generated and subjected to GBS. A total of 137,699,000 reads with an average of 357,376 reads per individual RIL were generated, which is equivalent to approximately 0.07-fold coverage of the maize B73 RefGen_V3 genome for each individual RIL. A high-density genetic map was constructed using 4183 bin markers (100-Kb intervals with no recombination events). The total genetic distance covered by the linkage map was 1545.65 cM and the average distance between adjacent markers was 0.37 cM with a physical distance of about 0.51 Mb. Our results demonstrated a relatively high degree of collinearity between the genetic map and the B73 reference genome. The quality and accuracy of the bin map for QTL detection was verified by the mapping of a known gene, pericarp color 1 (P1), which controls the color of the cob, with a high LOD value of 80.78 on chromosome 1. Using this high-density bin map, 35 QTL affecting plant architecture, including 14 for plant height, 14 for ear height, and seven for internode number were detected across three environments. Interestingly, pQTL10, which influences all three of these traits, was stably detected in three environments on chromosome 10 within an interval of 14.6 Mb. Two MYB transcription factor genes, GRMZM2G325907 and GRMZM2G108892, which might regulate plant cell wall metabolism are the candidate genes for qPH10. Conclusions Here, an ultra-high density accurate linkage map for a set of maize RILs was constructed using a GBS strategy. This map will facilitate identification of genes and exploration of QTL for plant architecture in maize. It will also be helpful for further research into the mechanisms that control plant architecture while also providing a basis for marker-assisted selection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2555-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Chaoshu Zhang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Yu Zhou
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Zhenhua Wang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Xing Zeng
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Hong Di
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Shihuang Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| |
Collapse
|
48
|
Liu S, Gao P, Zhu Q, Luan F, Davis AR, Wang X. Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data. BREEDING SCIENCE 2016; 66:244-59. [PMID: 27162496 PMCID: PMC4785002 DOI: 10.1270/jsbbs.66.244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 11/26/2015] [Indexed: 05/06/2023]
Abstract
Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). This study detected and converted SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon, for linkage map construction and quantitative trait locus (QTL) analysis. Two inbred lines, Cream of Saskatchewan (COS) and LSW-177 had been re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. 88.7% and 78.5% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. Comparative assembled genome data analysis provided 225,693 and 19,268 SNPs and indels between the two materials. 532 pairs of CAPS markers were designed with 16 restriction enzymes, among which 271 pairs of primers gave distinct bands of the expected length and polymorphic bands, via PCR and enzyme digestion, with a polymorphic rate of 50.94%. Using the new CAPS markers, an initial CAPS-based genetic linkage map was constructed with the F2 population, spanning 1836.51 cM with 11 linkage groups and 301 markers. 12 QTLs were detected related to fruit flesh color, length, width, shape index, and brix content. These newly CAPS markers will be a valuable resource for breeding programs and genetic studies of watermelon.
Collapse
Affiliation(s)
- Shi Liu
- Horticulture College, Northeast Agricultural University,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
| | - Peng Gao
- Horticulture College, Northeast Agricultural University,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
| | - Qianglong Zhu
- Horticulture College, Northeast Agricultural University,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
| | - Feishi Luan
- Horticulture College, Northeast Agricultural University,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Corresponding author (e-mail: )
| | - Angela R. Davis
- South Central Agricultural Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture. Currently with HM. Clause,
9241 Mace Blvd, Davis, CA 95618,
USA
| | - Xiaolu Wang
- Horticulture College, Northeast Agricultural University,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
| |
Collapse
|
49
|
Wang L, Xia Q, Zhang Y, Zhu X, Zhu X, Li D, Ni X, Gao Y, Xiang H, Wei X, Yu J, Quan Z, Zhang X. Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map. BMC Genomics 2016; 17:31. [PMID: 26732604 PMCID: PMC4702397 DOI: 10.1186/s12864-015-2316-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/15/2015] [Indexed: 12/23/2022] Open
Abstract
Background Sesame is an important high-quality oil seed crop. The sesame genome was de novo sequenced and assembled in 2014 (version 1.0); however, the number of anchored pseudomolecules was higher than the chromosome number (2n = 2x = 26) due to the lack of a high-density genetic map with 13 linkage groups. Results We resequenced a permanent population consisting of 430 recombinant inbred lines and constructed a genetic map to improve the sesame genome assembly. We successfully anchored 327 scaffolds onto 13 pseudomolecules. The new genome assembly (version 2.0) included 97.5 % of the scaffolds greater than 150 kb in size present in assembly version 1.0 and increased the total pseudomolecule length from 233.7 to 258.4 Mb with 94.3 % of the genome assembled and 97.2 % of the predicted gene models anchored. Based on the new genome assembly, a bin map including 1,522 bins spanning 1090.99 cM was generated and used to identified 41 quantitative trait loci (QTLs) for sesame plant height and 9 for seed coat color. The plant height-related QTLs explained 3–24 % the phenotypic variation (mean value, 8 %), and 29 of them were detected in at least two field trials. Two major loci (qPH-8.2 and qPH-3.3) that contributed 23 and 18 % of the plant height were located in 350 and 928-kb spaces on Chr8 and Chr3, respectively. qPH-3.3, is predicted to be responsible for the semi-dwarf sesame plant phenotype and contains 102 candidate genes. This is the first report of a sesame semi-dwarf locus and provides an interesting opportunity for a plant architecture study of the sesame. For the sesame seed coat color, the QTLs of the color spaces L*, a*, and b* were detected with contribution rates of 3–46 %. qSCb-4.1 contributed approximately 39 % of the b* value and was located on Chr4 in a 199.9-kb space. A list of 32 candidate genes for the locus, including a predicted black seed coat-related gene, was determined by screening the newly anchored genome. Conclusions This study offers a high-density genetic map and an improved assembly of the sesame genome. The number of linkage groups and pseudomolecules in this assembly equals the number of sesame chromosomes for the first time. The map and updated genome assembly are expected to serve as a platform for future comparative genomics and genetic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2316-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Qiuju Xia
- Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China.
| | - Yanxin Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Xiaodong Zhu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Xiaofeng Zhu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Donghua Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Xuemei Ni
- Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China.
| | - Yuan Gao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Haitao Xiang
- Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China.
| | - Xin Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Jingyin Yu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Zhiwu Quan
- Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China.
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| |
Collapse
|
50
|
Nimmakayala P, Tomason YR, Abburi VL, Alvarado A, Saminathan T, Vajja VG, Salazar G, Panicker GK, Levi A, Wechter WP, McCreight JD, Korol AB, Ronin Y, Garcia-Mas J, Reddy UK. Genome-Wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map. FRONTIERS IN PLANT SCIENCE 2016; 7:1437. [PMID: 27713759 PMCID: PMC5031849 DOI: 10.3389/fpls.2016.01437] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/08/2016] [Indexed: 05/06/2023]
Abstract
Melon (Cucumis melo L.) is a phenotypically diverse eudicot diploid (2n = 2x = 24) has climacteric and non-climacteric morphotypes and show wide variation for fruit firmness, an important trait for transportation and shelf life. We generated 13,789 SNP markers using genotyping-by-sequencing (GBS) and anchored them to chromosomes to understand genome-wide fixation indices (Fst) between various melon morphotypes and genomewide linkage disequilibrium (LD) decay. The FST between accessions of cantalupensis and inodorus was 0.23. The FST between cantalupensis and various agrestis accessions was in a range of 0.19-0.53 and between inodorus and agrestis accessions was in a range of 0.21-0.59 indicating sporadic to wide ranging introgression. The EM (Expectation Maximization) algorithm was used for estimation of 1436 haplotypes. Average genome-wide LD decay for the melon genome was noted to be 9.27 Kb. In the current research, we focused on the genome-wide divergence underlying diverse melon horticultural groups. A high-resolution genetic map with 7153 loci was constructed. Genome-wide segregation distortion and recombination rate across various chromosomes were characterized. Melon has climacteric and non-climacteric morphotypes and wide variation for fruit firmness, a very important trait for transportation and shelf life. Various levels of QTLs were identified with high to moderate stringency and linked to fruit firmness using both genome-wide association study (GWAS) and biparental mapping. Gene annotation revealed some of the SNPs are located in β-D-xylosidase, glyoxysomal malate synthase, chloroplastic anthranilate phosphoribosyltransferase, and histidine kinase, the genes that were previously characterized for fruit ripening and softening in other crops.
Collapse
Affiliation(s)
- Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Yan R. Tomason
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
- Department of Selection and Seed Production, Dnepropetrovsk State Agrarian and Economic UniversityDnepropetrovsk, Ukraine
| | - Venkata L. Abburi
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Alejandra Alvarado
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Thangasamy Saminathan
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Venkata G. Vajja
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Germania Salazar
- Department of Agriculture, Alcorn State UniversityLorman, MS, USA
| | | | - Amnon Levi
- U.S. Vegetable Laboratory, United States Department of Agriculture, Agricultural Research ServiceCharleston, SC, USA
| | - William P. Wechter
- U.S. Vegetable Laboratory, United States Department of Agriculture, Agricultural Research ServiceCharleston, SC, USA
| | | | - Abraham B. Korol
- Department of Evolutionary and Environmental Biology, Haifa UniversityHaifa, Israel
| | - Yefim Ronin
- Department of Evolutionary and Environmental Biology, Haifa UniversityHaifa, Israel
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institute for Food and Agricultural Research and Technology-Universitat Autònoma de Barcelona-Universitat de BarcelonaBarcelona, Spain
| | - Umesh K. Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
- *Correspondence: Umesh K. Reddy
| |
Collapse
|