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Peach, Almond, and Their Wild Relatives: Evolution and Domestication in Prunus Subgenus Amygdalus (Rosaceae).

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Peach, Almond, and Their Wild Relatives: Evolution and Domestication in Prunus Subgenus Amygdalus (Rosaceae)./
作者:	Velasco, Dianne M.
出版者:	Ann Arbor : ProQuest Dissertations & Theses, : 2019,
面頁冊數:	105 p.
附註:	Source: Dissertations Abstracts International, Volume: 81-04, Section: B.
Contained By:	Dissertations Abstracts International81-04B.
標題:	Genetics. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=13896317
ISBN:	9781088300978

Peach, Almond, and Their Wild Relatives: Evolution and Domestication in Prunus Subgenus Amygdalus (Rosaceae).
Velasco, Dianne M.

Peach, Almond, and Their Wild Relatives: Evolution and Domestication in Prunus Subgenus Amygdalus (Rosaceae). - Ann Arbor : ProQuest Dissertations & Theses, 2019 - 105 p.

Source: Dissertations Abstracts International, Volume: 81-04, Section: B.

Thesis (Ph.D.)--University of California, Davis, 2019.

This item must not be sold to any third party vendors.

Prunus L. (Rosaceae), a genus with approximately 200 insect-pollinated tree and shrub species, is distributed across mostly temperate regions. The Prunus subgenus Amygdalus, found in the temperate latitudes of Asia, includes species with differing mating systems and domestication status, both of which result in variability in genome size and genetic diversity among species in the subgenus. While many evolutionary forces have been examined in annual species, genome evolution is not as well studied in perennial species. However, comparisons of available data from studies of domesticated annuals and perennials have noted patterns that differ by life history. Our objective is to examine the genomes of species in Prunus subgenus Amygdalus to better understand evolution across the subgenus, both among clades and by domestication status. First we made a comparative investigation of the domesticates, P. dulcis (almond) and P. persica (peach), to understand whether domestication had similar effects on the genomes of these species. To then place our domestication results into a broad evolutionary context we investigated a representative sampling of species from both sections of Prunus subgenus Amygdalus.Independently domesticated approximately 5000 BP, Prunus dulcis (L.) Batsch (almond) and P. persica (Mill.) D. A. Webb (peach) are interfertile species that originated in western and eastern Asia, respectively. To gain insight into domestication in these species, and whether or not regions showing evidence of selection are shared, we performed compar- ative genome scans of these domesticated species. In addition to morphology, population structure analyses clearly separated P. dulcis and P. persica as well as identified additional population structure within each species. The species-specific population structure corresponds to centers of origin and diversity, such as East, Central, and West Asia, Europe, and the Americas. We estimated a basic divergence time of approximately 8 Ma which coincides with geologic activity contributing to uplift in the northwestern region of the Tibetan Plateau. Genetic diversity in P. dulcis is approximately seven-fold that of P. persica, which follows expectations given their mating systems. Demography estimates of the past 1000 to 20 M years, or approximately 100 to 2 M generations, show that P. dulcis experienced a bottleneck approximately 20 Kya followed by population expansion, possibly reflecting population recovery following the last glacial maximum, whereas P. persica suffered a decline beginning approximately 2 Ma that continues into the recent past, possibly reflecting an increase in selfing. While P. dulcis and P. persica do share some genomic regions of potential interest, we found little evidence for convergence in putative candidate loci under selection during domestication. However, loci not shared between these domesticated species may reflect evolution of the species post divergence or divergent selection during domestication.To investigate whether our findings in the domesticates, P. dulcis and P. persica, reflect patterns found in their respective sections (Amygdalus and Persica, respectively) within subgenus Amygdalus, we examined phylogeny, demography, and selection using multiple species of the same subgenus. We used P. argentea (Lam.) Rehder, P. bucharica (Korsh.) B. Fedtsch. ex Rehder, P. kuramica (Korsh.) Kitam., and P. arabica (Olivier) Meikle from Section Amygdalus and P. davidiana (Carr.) Franch, P. ferganensis (Kostina & Rjabov) Y.Y.Yao, P. kansuensis Rehder, P. mira Koehne, and P. tangutica (Batalin) Koehne from Section Persica to first construct a phylogeny from genome-wide variants, using P. cerasifera Ehrh. (subgenus Prunus) as the outgroup species. We then utilized this to investigate demography and selection within and across clades and groups.The phylogeny clearly divides Sections Amygdalus and Persica and further subdivides Section Persica into two subclades. One subclade consists of P. kansuensis, P. persica, and P. ferganensis while the second subclade includes P. davidiana, P. mira, and P. tangutica. The placement of P. tangutica in Section Persica is similar to recent studies although it has historically been place in Section Amygdalus due to having a dry dehiscent fruit at maturity, like other Section Amygdalus species. There are two pairs of species showing close relationships, P. persica with P. ferganensis and P. argentea with P. kuramica. The pairing of P. persica and P. ferganensis aligns with recent studies identifying P. ferganensis as a geographically separated population of P. persica. In contrast, the pairing of P. argentea and P. kuramica is likely a case of misidentification at collection or addition to the germplasm collection due to the phenotype of the P. argentea accession having a greater morphological similarity to that of P. kuramica than that of P. argentea.Demographic patterns of effective population size (Ne) in species across the subgenus roughly correlated with geologic activity and climatic changes. However, after the most recent subgenus-wide reduction between 1500 to 5000 generations ago (15 to 50 Ka), Ne of both domesticates increased rapidly to the present, suggesting population expansion due to recovery after the last glacial maximum and, possibly, pre-domestication cultivation. Wild species also had a decline in Ne followed by expansion, though their populations neither expanded at the same rate nor to the same level as the domesticates. However, sample sizes of the domesticates is larger than any wild species thus the software is better able to model the more recent past. As would be expected, the self-compatible wild species, P. mira, P. kansuensis, and P. ferganensis, had lower Ne than P. davidiana, the self-incompatible wild species in the subgenus available for modeling. However, the Ne in P. persica was higher than the other self-compatible species, which may be due to the influence of utilization of complex pedigrees and diverse germplasm use in modern breeding programs.Selection was detected in 3394 or 12.23% (FDR-adjusted p < 0.05) of the 27747 successfully tested genic loci. Of these, 1112 were found to be under selection along branches of the phylogenetic tree. There were 566 and 456 genes in Sections Amygdalus and Persica, respectively, divergently selected, while the outgroup species, P. cerasifera, diverged from subgenus Amygdalus species at 166 selected genes. Within Section Persica 94 genes were divergently selected in the kansuensis-persica-ferganensis subclade, and 224 in the mira-davidiana-tangutica subclade. Overall species had between 72 and 390 genes showing evidence of selection and between 3 and 244 showing evidence of divergent selection. Divergence between domesticates and wild species within Sections Amygdalus and Persica found the wild species diverged from their domesticated relatives at 181 and 383 genes, respectively. However domesticates only converged at two genes under selection, which was less than expected by chance. Gene ontology of all 3394 genes showing evidence of selection identified 50 significant (FDR < 0.05, p < 0.05) terms, primarily cell death and signaling, while annotation of these genes suggested many were involved in immune response or disease resistance. Divergence of genes between sections suggest they may be important for adaptation with the greatest difference between west and east Asia being annual precipitation.Here we illustrate the use of genome sequencing to examine domestication, evolution, and selection to provide the potential for beginning to address adaptation in tree species with more feasibility than some traditional experimental designs. While genes exhibiting signatures of selection in the domesticates P. dulcis and P.

ISBN: 9781088300978Subjects--Topical Terms:

530508
Genetics.
Subjects--Index Terms:

Almond

Peach, Almond, and Their Wild Relatives: Evolution and Domestication in Prunus Subgenus Amygdalus (Rosaceae).
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245 1 0 $a Peach, Almond, and Their Wild Relatives: Evolution and Domestication in Prunus Subgenus Amygdalus (Rosaceae).
260 1 $a Ann Arbor : $b ProQuest Dissertations & Theses, $c 2019
300 $a 105 p.
500 $a Source: Dissertations Abstracts International, Volume: 81-04, Section: B.
500 $a Advisor: Ross-Ibarra, Jeffrey.
502 $a Thesis (Ph.D.)--University of California, Davis, 2019.
506 $a This item must not be sold to any third party vendors.
520 $a Prunus L. (Rosaceae), a genus with approximately 200 insect-pollinated tree and shrub species, is distributed across mostly temperate regions. The Prunus subgenus Amygdalus, found in the temperate latitudes of Asia, includes species with differing mating systems and domestication status, both of which result in variability in genome size and genetic diversity among species in the subgenus. While many evolutionary forces have been examined in annual species, genome evolution is not as well studied in perennial species. However, comparisons of available data from studies of domesticated annuals and perennials have noted patterns that differ by life history. Our objective is to examine the genomes of species in Prunus subgenus Amygdalus to better understand evolution across the subgenus, both among clades and by domestication status. First we made a comparative investigation of the domesticates, P. dulcis (almond) and P. persica (peach), to understand whether domestication had similar effects on the genomes of these species. To then place our domestication results into a broad evolutionary context we investigated a representative sampling of species from both sections of Prunus subgenus Amygdalus.Independently domesticated approximately 5000 BP, Prunus dulcis (L.) Batsch (almond) and P. persica (Mill.) D. A. Webb (peach) are interfertile species that originated in western and eastern Asia, respectively. To gain insight into domestication in these species, and whether or not regions showing evidence of selection are shared, we performed compar- ative genome scans of these domesticated species. In addition to morphology, population structure analyses clearly separated P. dulcis and P. persica as well as identified additional population structure within each species. The species-specific population structure corresponds to centers of origin and diversity, such as East, Central, and West Asia, Europe, and the Americas. We estimated a basic divergence time of approximately 8 Ma which coincides with geologic activity contributing to uplift in the northwestern region of the Tibetan Plateau. Genetic diversity in P. dulcis is approximately seven-fold that of P. persica, which follows expectations given their mating systems. Demography estimates of the past 1000 to 20 M years, or approximately 100 to 2 M generations, show that P. dulcis experienced a bottleneck approximately 20 Kya followed by population expansion, possibly reflecting population recovery following the last glacial maximum, whereas P. persica suffered a decline beginning approximately 2 Ma that continues into the recent past, possibly reflecting an increase in selfing. While P. dulcis and P. persica do share some genomic regions of potential interest, we found little evidence for convergence in putative candidate loci under selection during domestication. However, loci not shared between these domesticated species may reflect evolution of the species post divergence or divergent selection during domestication.To investigate whether our findings in the domesticates, P. dulcis and P. persica, reflect patterns found in their respective sections (Amygdalus and Persica, respectively) within subgenus Amygdalus, we examined phylogeny, demography, and selection using multiple species of the same subgenus. We used P. argentea (Lam.) Rehder, P. bucharica (Korsh.) B. Fedtsch. ex Rehder, P. kuramica (Korsh.) Kitam., and P. arabica (Olivier) Meikle from Section Amygdalus and P. davidiana (Carr.) Franch, P. ferganensis (Kostina & Rjabov) Y.Y.Yao, P. kansuensis Rehder, P. mira Koehne, and P. tangutica (Batalin) Koehne from Section Persica to first construct a phylogeny from genome-wide variants, using P. cerasifera Ehrh. (subgenus Prunus) as the outgroup species. We then utilized this to investigate demography and selection within and across clades and groups.The phylogeny clearly divides Sections Amygdalus and Persica and further subdivides Section Persica into two subclades. One subclade consists of P. kansuensis, P. persica, and P. ferganensis while the second subclade includes P. davidiana, P. mira, and P. tangutica. The placement of P. tangutica in Section Persica is similar to recent studies although it has historically been place in Section Amygdalus due to having a dry dehiscent fruit at maturity, like other Section Amygdalus species. There are two pairs of species showing close relationships, P. persica with P. ferganensis and P. argentea with P. kuramica. The pairing of P. persica and P. ferganensis aligns with recent studies identifying P. ferganensis as a geographically separated population of P. persica. In contrast, the pairing of P. argentea and P. kuramica is likely a case of misidentification at collection or addition to the germplasm collection due to the phenotype of the P. argentea accession having a greater morphological similarity to that of P. kuramica than that of P. argentea.Demographic patterns of effective population size (Ne) in species across the subgenus roughly correlated with geologic activity and climatic changes. However, after the most recent subgenus-wide reduction between 1500 to 5000 generations ago (15 to 50 Ka), Ne of both domesticates increased rapidly to the present, suggesting population expansion due to recovery after the last glacial maximum and, possibly, pre-domestication cultivation. Wild species also had a decline in Ne followed by expansion, though their populations neither expanded at the same rate nor to the same level as the domesticates. However, sample sizes of the domesticates is larger than any wild species thus the software is better able to model the more recent past. As would be expected, the self-compatible wild species, P. mira, P. kansuensis, and P. ferganensis, had lower Ne than P. davidiana, the self-incompatible wild species in the subgenus available for modeling. However, the Ne in P. persica was higher than the other self-compatible species, which may be due to the influence of utilization of complex pedigrees and diverse germplasm use in modern breeding programs.Selection was detected in 3394 or 12.23% (FDR-adjusted p < 0.05) of the 27747 successfully tested genic loci. Of these, 1112 were found to be under selection along branches of the phylogenetic tree. There were 566 and 456 genes in Sections Amygdalus and Persica, respectively, divergently selected, while the outgroup species, P. cerasifera, diverged from subgenus Amygdalus species at 166 selected genes. Within Section Persica 94 genes were divergently selected in the kansuensis-persica-ferganensis subclade, and 224 in the mira-davidiana-tangutica subclade. Overall species had between 72 and 390 genes showing evidence of selection and between 3 and 244 showing evidence of divergent selection. Divergence between domesticates and wild species within Sections Amygdalus and Persica found the wild species diverged from their domesticated relatives at 181 and 383 genes, respectively. However domesticates only converged at two genes under selection, which was less than expected by chance. Gene ontology of all 3394 genes showing evidence of selection identified 50 significant (FDR < 0.05, p < 0.05) terms, primarily cell death and signaling, while annotation of these genes suggested many were involved in immune response or disease resistance. Divergence of genes between sections suggest they may be important for adaptation with the greatest difference between west and east Asia being annual precipitation.Here we illustrate the use of genome sequencing to examine domestication, evolution, and selection to provide the potential for beginning to address adaptation in tree species with more feasibility than some traditional experimental designs. While genes exhibiting signatures of selection in the domesticates P. dulcis and P.
520 $a persica have limited overlap, when examined in conjunction with closely related wild species, we are able to place them in a more comprehensive evolutionary context. We are then able to identify genes that appear to be under selection within their respective sections, Amygdalus and Persica, highlighting evolutionary paths possibly leading to domestication of P. dulcis and P. persica. Thus we can identify loci important for differentiation of the domesticates from their closest wild relatives that broadly occupy similar climates, which may suggest important genes in adaptation, and divergence of the taxonomic sections. While there is still much to learn about subgenus Amygdalus we may begin to utilize some of the information gained here to expand our understanding of evolution in insect-pollinated, deciduous tree species. With the high degree of interfertility among species in this subgenus we may be able to start applying the knowledge gained here to improve scion or rootstocks of P. dulcis and P. persica.
590 $a School code: 0029.
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650 4 $a Plant sciences. $3 3173832
650 4 $a Agriculture. $3 518588
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650 4 $a Horticulture. $3 555447
650 4 $a Molecular biology. $3 517296
650 4 $a Ecology. $3 516476
650 4 $a Plant pathology. $3 3174872
653 $a Almond
653 $a Amygdalus
653 $a Domestication
653 $a Peach
653 $a Prunus
653 $a Genome evolution
653 $a Adaptation
653 $a Deciduous tree species
653 $a Insect-pollinated trees
653 $a Disease resistance
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710 2 $a University of California, Davis. $b Genetics. $3 1676913
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