Integrative Analysis of the Metabolome and Transcriptome of a Cultivated Pepper and Its Wild Progenitor Chiltepin (Capsicum annuum L. var. glabriusculum) Revealed the Loss of Pungency During Capsicum Domestication

Pungency is a unique characteristic of chili peppers (Capsicum spp.) caused by capsaicinoids. The evolutionary emergence of pungency is thought to be a derived trait within the genus Capsicum. However, it is not well-known how pungency has varied during Capsicum domestication and specialization. In this study, we applied a comparative metabolomics along with transcriptomics analysis to assess various changes between two peppers (a mildly pungent cultivated pepper BB3 and its hot progenitor chiltepin) at four stages of fruit development, focusing on pungency variation. A total of 558 metabolites were detected in two peppers. In comparison with chiltepin, capsaicinoid accumulation in BB3 was almost negligible at the early stage. Next, 412 DEGs associated with the capsaicinoid accumulation pathway were identified through coexpression analysis, of which 18 genes (14 TFs, 3 CBGs, and 1 UGT) were deemed key regulators due to their high coefficients. Based on these data, we speculated that downregulation of these hub genes during the early fruit developmental stage leads to a loss in pungency during Capsicum domestication (from chiltepin to BB3). Of note, a putative UDP-glycosyltransferase, GT86A1, is thought to affect the stabilization of capsaicinoids. Our results lay the foundation for further research on the genetic diversity of pungency traits during Capsicum domestication and specialization.

Evaluation of Seed Dormancy, One of the Key Domestication Traits in Chickpea

Legume seed dormancy has been altered during the domestication process, resulting in non-dormant seeds with a testa that is readily permeable for water. Ultimately, this provides fast and uniform germination, in contrast to dormant seeds of the wild progenitor. To date, germination and seed dormancy were studied mostly in relation to two types of cultivated chickpea: kabuli and desi. We studied seed dormancy, from physiological and anatomical perspectives, in chickpea crops and compared cultivated chickpeas to the wild chickpea progenitor and set of recombinant inbred lines (RIL). There was significant difference in the macrosclereid length of parental genotypes. Cultivated chickpea (C. arietinum, ICC4958) had mean of 125 µm, while wild C. reticulatum (PI48977) had a mean of 165 µm. Histochemical staining of the seed coat also showed differences, mainly in terms of Sudan Red detection of lipidic substances. Imbibition and germination were tested and several germination coefficients were calculated. Cultivated chickpea seeds imbibed readily within 24 h, while the germination percentage of wild chickpea at various times was 36% (24 h), 46% (48 h), 60% (72 h) and reached 100% only after 20 days. RIL lines showed a broader distribution. This knowledge will ultimately lead to the identification of the underlying molecular mechanism of seed dormancy in chickpea, as well as allowing comparison to phylogenetically related legumes, such as pea, lentil and faba bean, and could be utilized in chickpea breeding programs.

Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement

Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

Phenotypic Evolution of The Wild Progenitor of Cultivated Barley (Hordeum Vulgare Subsp. Spontaneum (C. Koch) Thell.) Across Bioclimatic Regions In Jordan

Climate change affects the evolutionary potential and the survival of wild plant populations by acting on fitness traits. Resurrection approach was applied to investigate the phenotypic changes during the evolution of the wild progenitor of cultivated barley, Hordeum spontaneum K. Koch in Jordan. We compared 40 Hordeum spontaneum K. Koch populations collected in Jordan in 1991 with 40 Hordeum spontaneum K. Koch populations collected from the same sites in 2014. In the comparison we included seven Hordeum vulgare checks (one local landrace and six improved varieties). The analysis of the phenotypic data showed that the populations were aggregated according to their ecological geographical pattern in two groups with a significant (p < 0.0001) correlation between groups. Four heritable traits, namely plant height, biological yield, number of tillers, and awn length, determined the phenotypic structure of the populations. The two populations collected at 23 years distance, diverged in two distinctive phenotypic structure categories; a conserved structure and an evolved structure with a reduction in the phenotypic trait diversity in the population collected in 2014. These results reveal the value of combining phenotypic and environmental data to understand the evolution and adaptation of the population to climate change over a long period and the consequences on the wild progenitor of cultivated barley collection to avoid loss of genetic materials.

Targeted Sequencing Suggests Wild-Crop Gene Flow Is Central to Different Genetic Consequences of Two Independent Pumpkin Domestications

Studies of domestication genetics enrich our understanding of how domestication shapes genetic and morphological diversity. We characterized patterns of genetic variation in two independently domesticated pumpkins and their wild progenitors to assess and compare genetic consequences of domestication. To compare genetic diversity pre- and post-domestication and to identify genes targeted by selection during domestication, we analyzed ∼15,000 SNPs of 48 unrelated accessions, including wild, landrace, and improved lines for each of two pumpkin species, Cucurbita argyrosperma and Cucurbita maxima. Genetic diversity relative to its wild progenitor was reduced in only one domesticated subspecies, C. argyrosperma ssp. argyrosperma. The two species have different patterns of genetic structure across domestication status. Only 1.5% of the domestication features identified for both species were shared between species. These findings suggest that ancestral genetic diversity, wild-crop gene flow, and domestication practices shaped the genetic diversity of two similar Cucurbita crops in different ways, adding to our understanding of how genetic diversity changes during the processes of domestication and how trait improvement impacts the breeding potential of modern crops.

Anatomy and Histochemistry of Seed Coat Development of Wild (Pisum sativum subsp. elatius (M. Bieb.) Asch. et Graebn. and Domesticated Pea (Pisum sativum subsp. sativum L.)

In angiosperms, the mature seed consists of embryo, endosperm, and a maternal plant-derived seed coat (SC). The SC plays a role in seed filling, protects the embryo, mediates dormancy and germination, and facilitates the dispersal of seeds. SC properties have been modified during the domestication process, resulting in the removal of dormancy, mediated by SC impermeability. This study compares the SC anatomy and histochemistry of two wild (JI64 and JI1794) and two domesticated (cv. Cameor and JI92) pea genotypes. Histochemical staining of five developmental stages: 13, 21, 27, 30 days after anthesis (DAA), and mature dry seeds revealed clear differences between both pea types. SC thickness is established early in the development (13 DAA) and is primarily governed by macrosclereid cells. Polyanionic staining by Ruthenium Red indicated non homogeneity of the SC, with a strong signal in the hilum, the micropyle, and the upper parts of the macrosclereids. High peroxidase activity was detected in both wild and cultivated genotypes and increased over the development peaking prior to desiccation. The detailed knowledge of SC anatomy is important for any molecular or biochemical studies, including gene expression and proteomic analysis, especially when comparing different genotypes and treatments. Analysis is useful for other crop-to-wild-progenitor comparisons of economically important legume crops.

Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)

An understanding of the relationship between the cultivated apple (Malus domestica) and its primary wild progenitor species (M. sieversii) not only provides an understanding of how apples have been improved in the past, but may be useful for apple improvement in the future. We measured 10 phenotypes in over 1000 unique apple accessions belonging to M. domestica and M. sieversii from Canada’s Apple Biodiversity Collection. Using principal components analysis (PCA), we determined that M. domestica and M. sieversii differ significantly in phenotypic space and are nearly completely distinguishable as two separate groups. We found that M. domestica had a shorter juvenile phase than M. sieversii and that cultivated trees produced flowers and ripe fruit later than their wild progenitors. Cultivated apples were also 3.6 times heavier, 43% less acidic, and had 68% less phenolic content than wild apples. Using historical records, we found that apple breeding over the past 200 years has resulted in a trend towards apples that have higher soluble solids, are less bitter, and soften less during storage. Our results quantify the significant changes in phenotype that have taken place since apple domestication, and provide evidence that apple breeding has led to continued phenotypic divergence of the cultivated apple from its wild progenitor species.