Excess allozyme homozygosity and breeding population structure in the Mussel Mytilus californianus

Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low FST (0.0285–0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies.

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Isonymy and population structure of Irish isolates during the 1890s

Journal of Biosocial Science ◽

10.1017/s002193200001405x ◽

1982 ◽

Vol 14 (2) ◽

pp. 241-247 ◽

Cited By ~ 14

Author(s):

John H. Relethford

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Isolation By Distance ◽

Breeding Population ◽

Isolated Populations ◽

Estimated Parameters ◽

Distance Model ◽

Local Breeding ◽

And Migration ◽

Close Fit

SummaryThe estimation of genetic similarity from correspondence of surnames (isonymy) allows investigation of historical population structure. This study uses surname data from seven isolates located along the west coast of Ireland during the 1890s to assess geographic and historic influences on population structure. Observed genetic variation among populations shows a close fit with the expected isolation by distance model, with estimated parameters of isolation and migration being similar to those obtained in other studies of isolated populations. Local genetic variation appears to be due primarily to the size of the local breeding population, with deviations being explained in terms of recent emigration.

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Population structure of the Sahiwal breed in Pakistan

Animal Science ◽

10.1017/s1357729800008304 ◽

1995 ◽

Vol 60 (2) ◽

pp. 163-168 ◽

Cited By ~ 6

Author(s):

A. Dahlin ◽

U. N. Khan ◽

A. H. Zafar ◽

M. Saleem ◽

M. A. Chaudhry ◽

...

Keyword(s):

Population Structure ◽

Population Size ◽

Effective Population Size ◽

Breeding Population ◽

Effective Population ◽

Data Set ◽

Inbreeding Coefficients ◽

Sahiwal Cows ◽

The Mean ◽

Average Population Size

AbstractThe present study was undertaken to assist conservation and improvement schemes in the Sahiwal breed of cattle in Pakistan. A data set, consisting of records of 244 pure Sahiwal breeding bulls and 5247 cows, the latter representing about 80% of all recorded Sahiwal cows in Pakistan born during a period covering about 20 years, was analysed with regard to inbreeding, additive relationships, effective population size and generation intervals. Average inbreeding coefficients of 1224 cows and 49 bulls, for which at least the grandparents and great-grandsires were known, were 0·043 and 0·046, respectively. About two-thirds of the inbreeding was due to matings between animals with parents or grandparents in common. The mean additive relationship among the cows was 0·062, with within-herd averages ranging from 0·087 to 0·358. The average population size in a subdata set of recorded Sahiwal cattle from 1980 to 1984 was 1612, whereas the most likely estimate of the effective population size was about 30 animals for the same active breeding population. The study indicated the immediate need for an active conservation programme whereby the Sahiwal subpopulations of India and Kenya also should be involved.

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Genetic Diversity and Population Structure of Mesoamerican Scarlet Macaws in an Ex Situ Breeding Population in Mexico

Diversity ◽

10.3390/d14010054 ◽

2022 ◽

Vol 14 (1) ◽

pp. 54

Author(s):

Patricia Escalante-Pliego ◽

Noemí Matías-Ferrer ◽

Patricia Rosas-Escobar ◽

Gabriela Lara-Martínez ◽

Karol Sepúlveda-González ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Breeding Population ◽

Ex Situ ◽

Captive Population ◽

Genetic Lineages ◽

In Captivity ◽

Breeding Groups ◽

Ara Macao ◽

Scarlet Macaw

Given the interest in the conservation of the Mesoamerican scarlet macaw (Ara macao cyanoptera), the Xcaret Park formed an initial reproductive population about 30 years ago, which has progressively grown to a considerable population in captivity. In this work, we focus on the evaluation of the genetic diversity of the captive population, taking two groups into account: its founding (49) and the current breeding individuals (166). The genetic analysis consisted of genotyping six nuclear microsatellite loci that are characterized by their high variability. Tests for all loci revealed a Hardy–Weinberg equilibrium in four loci of the founders and in no loci of the breeding groups. The results showed that the genetic variation in the Xcaret population was relatively high (founders He = 0.715 SE = 0.074, breeding pairs He = 0.763 SE = 0.050), with an average polymorphism of 7.5 (4–10) alleles per locus in founders and 8.3 (4–14) in breeding pairs. No significant differences in the evaluated genetic diversity indexes were found between both groups. This indicates that the genetic variability in Xcaret has been maintained, probably due to the high number of pairs and the reproductive management strategy. Bayesian analysis revealed five different genetic lineages present in different proportions in the founders and in the breeding pairs, but no population structure was observed between founders and breeding individuals. The analyzed captive individuals showed levels of genetic diversity comparable to reported values from Ara macao wild populations. These data indicate that the captive population has maintained a similar genetic diversity as the metapopulation in the Mayan Forest and is an important resource for reintroduction projects, some of which began more than five years ago and are still underway.

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Geographic variations in life-history characteristics of white-spotted charr (Salvelinus leucomaenis)

Canadian Journal of Zoology ◽

10.1139/z99-055 ◽

1999 ◽

Vol 77 (6) ◽

pp. 871-878 ◽

Cited By ~ 12

Author(s):

Shoichiro Yamamoto ◽

Kentaro Morita ◽

Akira Goto

Keyword(s):

Population Structure ◽

Breeding Population ◽

Relative Difference ◽

Population Variation ◽

Geographic Variations ◽

River Population ◽

Salvelinus Leucomaenis ◽

Breeding Populations ◽

Mature Parr ◽

Three Rivers

Breeding-population structure, age and size at maturity, age and size at smolting, and riverine growth rate were investigated for three populations of white-spotted charr (Salvelinus leucomaenis) in the Nairo, Haraki, and Takahara rivers in Japan. The breeding populations in the Nairo and Haraki rivers on Hokkaido Island exhibited size polymorphism, comprising smaller mature parr and larger migrants. On the other hand, the population in the Takahara River on central Honshu Island showed a monomorphic structure, being composed of mature parr only. Maturation at the parr stage was positively associated with body size. The patterns of length-specific maturation ratios in the three rivers were similar, although females matured at a larger size than males. Smolt sizes differed between the polymorphic populations in the Nairo and Haraki rivers, but size relationships between the sexes were similar in the two populations. The incidence of smolts of a given length within populations was much higher in the northern Nairo River population than in the more southerly Haraki River population. These observations indicate that among-population variation in the structure of white-spotted charr populations might be related to differences in the relative proportions of mature parr and smolts in the population. We suggest that the relative difference in size thresholds between smolting and maturation determines the relative incidence of mature parr and smolts, both within and among populations and between the sexes, which in turn regulates the breeding-population structure.

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Population structure, genetic diversity and linkage disequilibrium in a macadamia breeding population using SNP and silicoDArT markers

Tree Genetics & Genomes ◽

10.1007/s11295-019-1331-z ◽

2019 ◽

Vol 15 (2) ◽

Cited By ~ 6

Author(s):

Katie O’Connor ◽

Andrzej Kilian ◽

Ben Hayes ◽

Craig Hardner ◽

Catherine Nock ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Breeding Population

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Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

10.1101/826792 ◽

2019 ◽

Author(s):

Dorcus C Gemenet ◽

Mercy N Kitavi ◽

Maria David ◽

Dorcah Ndege ◽

Reuben T Ssali ◽

...

Keyword(s):

Quality Assurance ◽

Population Structure ◽

Virus Disease ◽

Essential Element ◽

Breeding Population ◽

Error Rates ◽

Breeding Programs ◽

Genetic Gains ◽

And Control ◽

Quality Assurance And Control

AbstractQuality assurance and control (QA/QC) is an essential element of a breeding program’s optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)’s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers fields. The study also enabled evaluation of CIP’s global breeding population structure and the effect of some of the most devastating biotic stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato.Key MessageA 36-SNP diagnostic marker set has been developed for quality assurance and control to support global sweetpotato breeding optimization efforts. Breeding population structure is shaped by sweetpotato virus disease prevalence.

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