1
|
Zhang L, Zhang HL, Chen Y, Nizamani MM, Wu T, Liu T, Zhou Q. Assessing genetic diversity in critically endangered Chieniodendron hainanense populations within fragmented habitats in Hainan. Sci Rep 2024; 14:6988. [PMID: 38523175 PMCID: PMC10961303 DOI: 10.1038/s41598-024-56630-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/08/2024] [Indexed: 03/26/2024] Open
Abstract
Habitat fragmentation has led to a reduction in the geographic distribution of species, making small populations vulnerable to extinction due to environmental, demographic, and genetic factors. The wild plant Chieniodendron hainanense, a species with extremely small populations, is currently facing endangerment and thus requires urgent conservation efforts. Understanding its genetic diversity is essential for uncovering the underlying mechanisms of its vulnerability and for developing effective conservation strategies. In our study, we analyzed 35 specimens from six different populations of C. hainanense using genotyping-by-sequencing (GBS) and single nucleotide polymorphism (SNP) methodologies. Our findings indicate that C. hainanense has limited genetic diversity. The observed heterozygosity across the populations ranged from 10.79 to 14.55%, with an average of 13.15%. We categorized the six populations of C. hainanense into two distinct groups: (1) Diaoluoshan and Baishaling, and (2) Wuzhishan, Huishan, Bawangling, and Jianfengling. The genetic differentiation among these populations was found to be relatively weak. The observed loss of diversity is likely a result of the effects of natural selection.
Collapse
Affiliation(s)
- Li Zhang
- Guizhou Normal University Museum, Guizhou Normal University, Guiyang, 550001, China
| | - Hai-Li Zhang
- Sanya Nanfan Research Institute, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Yukai Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
| | - Mir Muhammad Nizamani
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, 550001, China.
| | - Tingtian Wu
- Hainan Academy of Forestry, Hainan Academy of Mangrove, Haikou, 570228, China
| | - Tingting Liu
- Guizhou Normal University Museum, Guizhou Normal University, Guiyang, 550001, China
| | - Qin Zhou
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| |
Collapse
|
2
|
Vanvanhossou SFU, Scheper C, Dossa LH, Yin T, Brügemann K, König S. A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits. BMC Genomics 2020; 21:783. [PMID: 33176675 PMCID: PMC7656759 DOI: 10.1186/s12864-020-07170-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. RESULTS SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). CONCLUSIONS Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.
Collapse
Affiliation(s)
| | - Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Luc Hippolyte Dossa
- School of Science and Technics of Animal Production, Faculty of Agricultural Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany.
| |
Collapse
|
3
|
Strucken EM, Al-Mamun HA, Esquivelzeta-Rabell C, Gondro C, Mwai OA, Gibson JP. Genetic tests for estimating dairy breed proportion and parentage assignment in East African crossbred cattle. Genet Sel Evol 2017; 49:67. [PMID: 28899355 PMCID: PMC5596489 DOI: 10.1186/s12711-017-0342-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/30/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Smallholder dairy farming in much of the developing world is based on the use of crossbred cows that combine local adaptation traits of indigenous breeds with high milk yield potential of exotic dairy breeds. Pedigree recording is rare in such systems which means that it is impossible to make informed breeding decisions. High-density single nucleotide polymorphism (SNP) assays allow accurate estimation of breed composition and parentage assignment but are too expensive for routine application. Our aim was to determine the level of accuracy achieved with low-density SNP assays. METHODS We constructed subsets of 100 to 1500 SNPs from the 735k-SNP Illumina panel by selecting: (a) on high minor allele frequencies (MAF) in a crossbred population; (b) on large differences in allele frequency between ancestral breeds; (c) at random; or (d) with a differential evolution algorithm. These panels were tested on a dataset of 1933 crossbred dairy cattle from Kenya/Uganda and on crossbred populations from Ethiopia (N = 545) and Tanzania (N = 462). Dairy breed proportions were estimated by using the ADMIXTURE program, a regression approach, and SNP-best linear unbiased prediction, and tested against estimates obtained by ADMIXTURE based on the 735k-SNP panel. Performance for parentage assignment was based on opposing homozygotes which were used to calculate the separation value (sv) between true and false assignments. RESULTS Panels of SNPs based on the largest differences in allele frequency between European dairy breeds and a combined Nelore/N'Dama population gave the best predictions of dairy breed proportion (r2 = 0.962 to 0.994 for 100 to 1500 SNPs) with an average absolute bias of 0.026. Panels of SNPs based on the highest MAF in the crossbred population (Kenya/Uganda) gave the most accurate parentage assignments (sv = -1 to 15 for 100 to 1500 SNPs). CONCLUSIONS Due to the different required properties of SNPs, panels that did well for breed composition did poorly for parentage assignment and vice versa. A combined panel of 400 SNPs was not able to assign parentages correctly, thus we recommend the use of 200 SNPs either for breed proportion prediction or parentage assignment, independently.
Collapse
Affiliation(s)
- Eva M Strucken
- School of Environmental and Rural Science, University of New England, Armidale, 2350, Australia
| | - Hawlader A Al-Mamun
- School of Environmental and Rural Science, University of New England, Armidale, 2350, Australia
| | | | - Cedric Gondro
- Michigan State University, Animal Science, East Lansing, Michigan, 48824, USA
| | - Okeyo A Mwai
- International Livestock Research Institute, Nairobi, Kenya
| | - John P Gibson
- School of Environmental and Rural Science, University of New England, Armidale, 2350, Australia.
| |
Collapse
|
4
|
Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
Collapse
Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| |
Collapse
|
5
|
Eynard SE, Windig JJ, Hiemstra SJ, Calus MPL. Whole-genome sequence data uncover loss of genetic diversity due to selection. Genet Sel Evol 2016; 48:33. [PMID: 27080121 PMCID: PMC4831198 DOI: 10.1186/s12711-016-0210-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 03/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole-genome sequence (WGS) data give access to more complete structural genetic information of individuals, including rare variants, not fully covered by single nucleotide polymorphism chips. We used WGS to investigate the amount of genetic diversity remaining after selection using optimal contribution (OC), considering different methods to estimate the relationships used in OC. OC was applied to minimise average relatedness of the selection candidates and thus miminise the loss of genetic diversity in a conservation strategy, e.g. for establishment of gene bank collections. Furthermore, OC was used to maximise average genetic merit of the selection candidates at a given level of relatedness, similar to a genetic improvement strategy. In this study, we used data from 277 bulls from the 1000 bull genomes project. We measured genetic diversity as the number of variants still segregating after selection using WGS data, and compared strategies that targeted conservation of rare (minor allele frequency <5 %) versus common variants. RESULTS When OC without restriction on the number of selected individuals was applied, loss of variants was minimal and most individuals were selected, which is often unfeasible in practice. When 20 individuals were selected, the number of segregating rare variants was reduced by 29 % for the conservation strategy, and by 34 % for the genetic improvement strategy. The overall number of segregating variants was reduced by 30 % when OC was restricted to selecting five individuals, for both conservation and genetic improvement strategies. For common variants, this loss was about 15 %, while it was much higher, 72 %, for rare variants. Fewer rare variants were conserved with the genetic improvement strategy compared to the conservation strategy. CONCLUSIONS The use of WGS for genetic diversity quantification revealed that selection results in considerable losses of genetic diversity for rare variants. Using WGS instead of SNP chip data to estimate relationships slightly reduced the loss of rare variants, while using 50 K SNP chip data was sufficient to conserve common variants. The loss of rare variants could be mitigated by a few percent (up to 8 %) depending on which method is chosen to estimate relationships from WGS data.
Collapse
Affiliation(s)
- Sonia E Eynard
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands. .,GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,Centre for Genetic Resources, the Netherlands, Wageningen UR, P.O. Box 338, 3700 AH, Wageningen, The Netherlands.
| | - Jack J Windig
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.,Centre for Genetic Resources, the Netherlands, Wageningen UR, P.O. Box 338, 3700 AH, Wageningen, The Netherlands
| | - Sipke J Hiemstra
- Centre for Genetic Resources, the Netherlands, Wageningen UR, P.O. Box 338, 3700 AH, Wageningen, The Netherlands
| | - Mario P L Calus
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| |
Collapse
|
6
|
The effect of rare alleles on estimated genomic relationships from whole genome sequence data. BMC Genet 2015; 16:24. [PMID: 25887220 PMCID: PMC4365517 DOI: 10.1186/s12863-015-0185-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/24/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Relationships between individuals and inbreeding coefficients are commonly used for breeding decisions, but may be affected by the type of data used for their estimation. The proportion of variants with low Minor Allele Frequency (MAF) is larger in whole genome sequence (WGS) data compared to Single Nucleotide Polymorphism (SNP) chips. Therefore, WGS data provide true relationships between individuals and may influence breeding decisions and prioritisation for conservation of genetic diversity in livestock. This study identifies differences between relationships and inbreeding coefficients estimated using pedigree, SNP or WGS data for 118 Holstein bulls from the 1000 Bull genomes project. To determine the impact of rare alleles on the estimates we compared three scenarios of MAF restrictions: variants with a MAF higher than 5%, variants with a MAF higher than 1% and variants with a MAF between 1% and 5%. RESULTS We observed significant differences between estimated relationships and, although less significantly, inbreeding coefficients from pedigree, SNP or WGS data, and between MAF restriction scenarios. Computed correlations between pedigree and genomic relationships, within groups with similar relationships, ranged from negative to moderate for both estimated relationships and inbreeding coefficients, but were high between estimates from SNP and WGS (0.49 to 0.99). Estimated relationships from genomic information exhibited higher variation than from pedigree. Inbreeding coefficients analysis showed that more complete pedigree records lead to higher correlation between inbreeding coefficients from pedigree and genomic data. Finally, estimates and correlations between additive genetic (A) and genomic (G) relationship matrices were lower, and variances of the relationships were larger when accounting for allele frequencies than without accounting for allele frequencies. CONCLUSIONS Using pedigree data or genomic information, and including or excluding variants with a MAF below 5% showed significant differences in relationship and inbreeding coefficient estimates. Estimated relationships and inbreeding coefficients are the basis for selection decisions. Therefore, it can be expected that using WGS instead of SNP can affect selection decision. Inclusion of rare variants will give access to the variation they carry, which is of interest for conservation of genetic diversity.
Collapse
|
7
|
Rothschild MF, Plastow GS. Applications of genomics to improve livestock in the developing world. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.03.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
8
|
Amador C, Fernández J, Meuwissen TH. Advantages of using molecular coancestry in the removal of introgressed genetic material. Genet Sel Evol 2013; 45:13. [PMID: 23634969 PMCID: PMC3652759 DOI: 10.1186/1297-9686-45-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 04/23/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND When introgression of undesired exogenous genetic material occurs in a population intended to remain pure, actions are necessary to recover the original background. It has been shown that genome-wide information can replace pedigree information for different objectives and is a valuable tool in the fields of genetic conservation and breeding. In this simulation study, molecular information provided by 50 000 SNP was used to minimise the molecular coancestry between individuals of an admixed population and the foreign individuals that originally introgressed a native population in order to remove the exogenous DNA. RESULTS This management method, which detects the 'purest' individuals to be used as parents for the next generation, allowed recovery of the native genetic background to a great extent in all simulated scenarios. However, it also caused an increase in inbreeding larger than expected because of the lower number of individuals selected as parents and the higher coancestry between them. In scenarios involving several introgression events the method was more efficient than in those involving a single introgression event because part of the genetic information was mixed with the native genetic material for a shorter period. CONCLUSIONS Genome-wide information can be used to identify the purest individuals via the minimisation of molecular coancestry between individuals of the admixed and exogenous populations. Removal of the undesired genetic material is more efficient with a molecular-based approach than with a pedigree-based approach.
Collapse
Affiliation(s)
- Carmen Amador
- INIA, Ctra, De La Coruña Km, 7,5, Madrid, 28040, Spain.
| | | | | |
Collapse
|
9
|
Abstract
The genomics era has opened up exciting possibilities in the field of conservation biology by enabling genomic analyses of threatened species that previously were limited to model organisms. Next-generation sequencing (NGS) and the collection of genome-wide data allow for more robust studies of the demographic history of populations and adaptive variation associated with fitness and local adaptation. Genomic analyses can also advance management efforts for threatened wild and captive populations by identifying loci contributing to inbreeding depression and disease susceptibility, and predicting fitness consequences of introgression. However, the development of genomic tools in wild species still carries multiple challenges, particularly those associated with computational and sampling constraints. This review provides an overview of the most significant applications of NGS and the implications and limitations of genomic studies in conservation.
Collapse
Affiliation(s)
- Cynthia C Steiner
- Institute for Conservation Research, San Diego Zoo Global, Escondido, California 92027; ; ;
| | | | | | | |
Collapse
|
10
|
Relative breed contributions to neutral genetic diversity of a comprehensive representation of Iberian native cattle. Animal 2011; 5:1323-34. [DOI: 10.1017/s1751731111000267] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
|