Patterns of genomic changes with crop domestication and breeding

Shi, Junpeng; Lai, Jinsheng

doi:10.1016/j.pbi.2015.01.008

Cited by 81 publications

(50 citation statements)

References 72 publications

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“…Conservation of these species is a priority because of their importance in breeding programs (Andueza‐Noh et al., 2016; De Ron et al., 2015; Debouck, 2000; Rodriguez et al., 2015; Shi & Lai, 2015; Singh, Singh, & Dutta, 2014). In addition, further work is needed to reinforce knowledge regarding population genetics and the response to ecological or climate changes and to evaluate survival rates (Delgado‐Salinas & Gama‐López, 2015).…”

Section: Discussionmentioning

confidence: 99%

Climatic adaptation and ecological descriptors of wild beans from Mexico

Cerda-Hurtado

Máyek-Pérez

Muruaga‐Martínez

et al. 2018

Ecology and Evolution

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Despite its economic, social, biological, and cultural importance, wild forms of the genus Phaseolus are not well represented in germplasm banks, and they are at great risk due to changes in land use as well as climate change. To improve our understanding of the potential geographical distribution of wild beans (Phaseolus spp.) from Mexico and support in situ and ex situ conservation programs, we determined the climatic adaptation ranges of 29 species and two subspecies of Phaseolus collected throughout Mexico. Based on five biotic and 117 abiotic variables obtained from different databases—WorldClim, Global‐Aridity, and Global‐PET—we performed principal component and cluster analyses. Germplasm was distributed among 12 climatic types from a possible 28. The general climatic ranges were as follows: 8–3,083 m above sea level; 12.07–26.96°C annual mean temperature; 10.33–202.68 mm annual precipitation; 9.33–16.56 W/m2 of net radiation; 11.68–14.23 hr photoperiod; 0.06–1.57 aridity index; and 10–1,728 mm/month of annual potential evapotranspiration. Most descriptive variables (25) clustered species into two groups: One included germplasm from semihot climates, and the other included germplasm from temperate climates. Species clustering showed 45% to 54% coincidence with species previously grouped using molecular data. The species P. filiformis, P. purpusii, and P. maculatus were found at low‐humidity locations; these species could be used to improve our understanding of the extreme aridity adaptation mechanisms used by wild beans to avoid or tolerate climate change as well as to introgress favorable alleles into new cultivars adapted to hot, dry environments.

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Section: Discussionmentioning

confidence: 99%

Climatic adaptation and ecological descriptors of wild beans from Mexico

Cerda-Hurtado

Máyek-Pérez

Muruaga‐Martínez

et al. 2018

Ecology and Evolution

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“…There has been concerted interest in the last few years in the analysis of natural variation in plant species (Hunter et al, 2013;Marroni et al, 2014;Shi and Lai, 2015). Comparative studies of patterns of diversity can provide insights into the major factors that underlie mutational diversity among different plant taxa.…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii

et al. 2015

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We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ;3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates conservation of genes associated with core cellular functions, while genes in large gene families and poorly characterized genes show a greater incidence of major effect mutations. De novo assembly of unmapped reads recovered genes in the field isolates that are absent from the CC-503 assembly. The laboratory reference strains show a genomic pattern of polymorphism consistent with their origin as the recombinant progeny of a diploid zygospore. Large duplications or amplifications are a prominent feature of laboratory strains and appear to have originated under laboratory culture. Extensive natural variation offers a new source of genetic diversity for studies of Chlamydomonas, including naturally occurring alleles that may prove useful in studies of gene function and the dissection of quantitative genetic traits.

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“…It is obviously advantageous to 388 maximise the chances of finding an association by including as much genetic diversity 389 as possible in a mapping population. In the case of crop plants domestication results in 390 a loss of genetic diversity (Doebley et al, 2006;Shi and Lai, 2015), so there is much to 391 be gained by including field races and wild types in the construction of mapping 392 populations or RILs. The phenotypic data required for QTL mapping requires 393 measurements upon hundreds or thousands of individuals depending on the mapping 394 approach adopted, the precision of the phenotyping procedure compared to the 395 variability of the trait and the heritability of the trait.…”

Section: If Variation For a Quantitative Trait Such As Photosynthetimentioning

confidence: 99%