Conservation of adaptive potential and functional diversity

Hoelzel, A. Rus; Bruford, Michael William; Fleischer, Robert C.

doi:10.1007/s10592-019-01151-x

“…Average nucleotide diversity in the whole panel was 0.28 in this study, which was higher than reported for a global collection [19], but lower than the mean gene diversity (0.54) estimated using simple sequence repeat (SSR) markers in a pearl millet inbred germplasm association panel (PMiGAP) [31]. As adaptive evolution is implicated in reducing functional diversity [18], genetic distance among inbred lines derived from landraces grown in similar environments is expected to be low. Nevertheless, ecology and evolution work together to determine the population stability and maintain diversity within and among populations [21].…”

Section: Discussioncontrasting

confidence: 76%

Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

Kanfany

¹

,

Serba

²

,

Rhodes

³

et al. 2020

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Background: Genetic improvement of pearl millet is lagging behind most of the major crops. Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutritional quality. Genotyping a breeding population with high throughput markers enables exploration of genetic diversity, population structure, and linkage disequilibrium (LD) which are important preludes for marker-trait association studies and application of genomic-assisted breeding. Results: Genotyping-by-sequencing (GBS) libraries of 309 inbred lines derived from landraces and improved varieties from Africa and India generated 54,770 high quality single nucleotide polymorphism (SNP) markers. On average one SNP per 29 Kb was mapped in the reference genome, with the telomeric regions more densely mapped than the pericentromeric regions of the chromosomes. Population structure analysis using 30,208 SNPs evenly distributed in the genome divided 309 accessions into five subpopulations with different levels of admixture. Pairwise genetic distance (GD) between accessions varied from 0.09 to 0.33 with the average distance of 0.28. Rapid LD decay implied low tendency of markers inherited together. Genetic differentiation estimates were the highest between subgroups 4 and 5, and the lowest between subgroups 1 and 2. Conclusions: Population genomic analysis of pearl millet inbred lines derived from diverse geographic and agroecological features identified five subgroups mostly following pedigree differences with different levels of admixture. It also revealed the prevalence of high genetic diversity in pearl millet, which is very useful in defining heterotic groups for hybrid breeding, trait mapping, and holds promise for improving pearl millet for yield and nutritional quality. The short LD decay observed suggests an absence of persistent haplotype blocks in pearl millet. The diverse genetic background of these lines and their low LD make this set of germplasm useful for traits mapping.

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“…Average nucleotide diversity in the whole panel was 0.28 in this study, which was higher than reported for a global collection (Hu et al, 2015), but lower than the mean gene diversity (0.54) estimated using simple sequence repeat (SSR) markers in a pearl millet inbred germplasm association panel (PMiGAP) (Sehgal et al, 2015). As adaptive evolution is implicated in reducing functional diversity (Hoelzel et al, 2019), genetic distance among inbred lines derived from landraces grown in similar environments is expected to be low. Nevertheless, ecology and evolution work together to determine the population stability and maintain diversity within and among populations (Koch et al, 2014).…”

Section: Germplasm Resources and The Genetic Diversity Of A Crop Speccontrasting

confidence: 77%

Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

Kanfany

¹

,

Serba

²

,

Rhodes

³

et al. 2020

Preprint

0

View full text Add to dashboard Cite

Background: Genetic improvement of pearl millet is lagging behind most of the major crops. Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutritional quality. Genotyping a breeding population with high throughput markers enables exploration of genetic diversity, population structure, and linkage disequilibrium (LD) which are important preludes for marker-trait association studies and application of genomic-assisted breeding. Results: Genotyping-by-sequencing (GBS) libraries of 309 inbred lines derived from landraces and improved varieties from Africa and India generated 54,770 high quality single nucleotide polymorphism (SNP) markers. On average one SNP per 29 Kb was mapped in the reference genome, with the telomeric regions more densely mapped than the pericentromeric regions of the chromosomes. Population structure analysis using 30,208 SNPs evenly distributed in the genome divided 309 accessions into five subpopulations with different levels of admixture. Pairwise genetic distance (GD) between accessions varied from 0.09 to 0.33 with the average distance of 0.28. Rapid LD decay implied low tendency of markers inherited together. Genetic differentiation estimates were the highest between subgroups 4 and 5, and the lowest between subgroups 1 and 2. Conclusions: Population genomic analysis of pearl millet inbred lines derived from diverse geographic and agroecological features identified five subgroups mostly following pedigree differences with different levels of admixture. It also revealed the prevalence of high genetic diversity in pearl millet, which is very useful in defining heterotic groups for hybrid breeding, trait mapping, and holds promise for improving pearl millet for yield and nutritional quality. The short LD decay observed suggests an absence of persistent haplotype blocks in pearl millet. The diverse genetic background of these lines and their low LD make this set of germplasm useful for traits mapping.

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“…Using a reference genome guided approach in the Tasmanian devil enabled 2060 SNPs to be identified [84] much more quickly than a de novo approach. Aligning the RRS data to the reference genome provides the ability to identify genes which may be targets of future analysis, and to separate functional vs. non-functional genome diversity which could have conservation implications [94]. For example, the reference genome was able to identify candidate genes within a genomic region that displayed signatures of selection in RRS data [76], and to identify cancer-resistance candidate genes from phenotype association tests of RRS data [77] (Table 1).…”

Section: Conservation Applications As a Results Of A Reference Genomementioning

confidence: 99%

The Value of Reference Genomes in the Conservation of Threatened Species

Brandies

¹

,

Peel

²

,

Hogg

³

et al. 2019

Genes

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Conservation initiatives are now more crucial than ever—over a million plant and animal species are at risk of extinction over the coming decades. The genetic management of threatened species held in insurance programs is recommended; however, few are taking advantage of the full range of genomic technologies available today. Less than 1% of the 13505 species currently listed as threated by the International Union for Conservation of Nature (IUCN) have a published genome. While there has been much discussion in the literature about the importance of genomics for conservation, there are limited examples of how having a reference genome has changed conservation management practice. The Tasmanian devil (Sarcophilus harrisii), is an endangered Australian marsupial, threatened by an infectious clonal cancer devil facial tumor disease (DFTD). Populations have declined by 80% since the disease was first recorded in 1996. A reference genome for this species was published in 2012 and has been crucial for understanding DFTD and the management of the species in the wild. Here we use the Tasmanian devil as an example of how a reference genome has influenced management actions in the conservation of a species.

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Conservation of adaptive potential and functional diversity

Cited by 59 publications

References 36 publications

Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

The Value of Reference Genomes in the Conservation of Threatened Species

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