The genetic structure of a wild wheat population has remained associated with microhabitats over 36 years

Wild progenitors of major crops can help us understand domestication, and may also provide the genetic resources needed for ensuring food security in the face of climate change. We examined the genetic structure of a wild emmer wheat population, sampled over 36 years while both temperature and CO2 concentration increased significantly. The genotypes of 832 individuals revealed high genetic diversity over scales of tens of meters and were clustered spatially into ecological microhabitats. This pattern was remarkably stable over time. Simulations indicate that neutral processes alone are unlikely to fully explain the spatial and temporal stability of the population. These results are consistent with a role for local adaptation in shaping the fine-scale structure of plant populations, which is relevant for in-situ conservation strategies of biodiversity in nature.

GENETIC ANALYSIS OF QUALITATIVE AND QUANTITATIVE TRAITS AMONG PROGENIES OF ENSET CLONES ORIGINATED FROM SOUTHERN ETHIOPIA

<p>The present cultivated enset (<em>Ensete ventricosum</em>) clonal landraces in Ethiopia originated from few wild progenitors. However, enset has a mixed mode of reproduction in which, the wild enset reproduces sexually through seeds, while cultivated enset is generally propagated vegetatively. The objectives of this study were to determine the genetic structure of enset cultivars through genetic analysis of qualitative morphological traits and estimate their genetic variability by evaluating the quantitative agronomic traits data generated from progenies of cultivated and wild enset genotypes. Hence, seeds collected from six cultivated and four wild enset genotypes were used for this study. Data on four qualitative and six quantitative morphological traits were recorded from the progenies of the 10 enset genotypes. Progenies of seven enset genotypes segregated in a 3:1 segregation ratio while progenies of the remaining genotypes segregated differently for the qualitative traits considered. With regard to the quantitative traits, the progenies of the 10 enset genotypes differed significantly for five of the six traits except pseudostem length. The cultivated clones, in general performed better than that of the wild types. Moderate heritability (h2b) estimates and high genetic advances were obtained for leaf length (0.38, 62.0%), pseudostem circumference (0.35, 78.5%), and plant height (0.30, 19.1%) indicating selection for these traits indirectly improves economic yield of enset clones. This study demonstrated the possibility of creating genetic variation through selfing the existing enset genotypes for traits of interest and making improvements either through selection or crossing the elite types to develop novel enset cultivars.</p>

Novel Fusarium Wilt Resistance Genes Uncovered in the Wild Progenitors and Heirloom Cultivars of Strawberry

Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria × ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and wild octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here we show that resistance to both races is widespread and that resistance to race 1 is mediated by dominant genes (FW1, FW2, FW3, FW4, and FW5) on three non-homoeologous chromosomes (1A, 2B, and 6B). The resistance proteins encoded by these genes are not yet known; however, plausible candidates were identified that encode pattern recognition receptor or other proteins known to mediate gene-for-gene resistance in plants. High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic.

Global cultivation of wheat crops induces considerable shifts in the range and niche of species relative to their wild progenitors

Species’ range and niche play key roles in understanding ecological and biogeographical patterns, especially in projecting global biotic homogenization and potential distribution patterns of species under global change scenarios. However, few studies have investigated the ability of crop cultivation to influence potential range sizes and niche shifts of species. Wheat and its wild progenitors share the same origin and evolutionary history, and thus provide an excellent system to explore this topic. Using ensembled ecological niche models and niche dynamic models, we studied the potential range sizes of wheat and its wild progenitors, as well as their niche dynamics. Our results showed that wheat had larger range size and niche breadth than its wild progenitors, suggesting that wheat cultivation is a more powerful driver of range and niche expansion than natural niche evolution. Additionally, wheat and its wild progenitors occupied different niche positions, and the former did not conserve the niches inherited from the latter, implying that wheat cultivation considerably induces niche shifts. The niche dynamics between wheat and its wild progenitors were not only closely associated with cultivation but were also modified by the niche conservatism of its wild progenitors. In contrast to most invasive plants, wheat, as a global staple crop species, did not conserve the niche space inherited from its wild progenitors, suggesting that compared with most plant invasions, cultivation may have a stronger effect on niche shifts. Therefore, global niche shifts induced by crop cultivation need much more attention, though the underlying mechanisms require further study.

Shape Diversity of Olive Stone, Resulting from Domestication and Diversification, Unveils Traits of the Oldest Known, 7000-Years-Old Table Olives from Hishuley Carmel Site (Israel)

The first exploited and domesticated olive forms are still unknown. The exceptionally well-preserved stones from the submerged Hishuley Carmel site (Israel), dating from the middle of the 7th millennium BP, offer us the opportunity to study the oldest table olives discovered so far. We apply a geometrical morphometric analysis in reference to a collection of modern stones from supposed wild populations and traditional varieties of various origins, genetic lineages and uses. Analyses carried out on modern material allow to characterize the extent of stone morphological variation in the olive tree and differentiate distinct morphotypes. They also allow to discuss the status of supposed wild populations and interpret the divergence between groups of varieties and their wild progenitors in an evolutionary and biogeographical perspective. Shape of archaeological stones compared to the differentiation model, unveils morphological traits of olives most likely belonging to both wild olive trees and domesticated forms, some of them showing a notable domestication syndrome. This forms at the early stages of domestications, some of which surprisingly morphologically close to modern varieties, were probably used for dual use (production of olive oil and table olives), and possibly contributed to the dispersion of the olive tree throughout the Mediterranean Basin and to its subsequent diversification.

Footprints of Selection Derived From Temporal Heterozygosity Patterns in a Barley Nested Association Mapping Population

Nowadays, genetic diversity more than ever represents a key driver of adaptation to climate challenges like drought, heat, and salinity. Therefore, there is a need to replenish the limited elite gene pools with favorable exotic alleles from the wild progenitors of our crops. Nested association mapping (NAM) populations represent one step toward exotic allele evaluation and enrichment of the elite gene pool. We investigated an adaptive selection strategy in the wild barley NAM population HEB-25 based on temporal genomic data by studying the fate of 214,979 SNP loci initially heterozygous in individual BC1S3 lines after five cycles of selfing and field propagation. We identified several loci exposed to adaptive selection in HEB-25. In total, 48.7% (104,725 SNPs) of initially heterozygous SNP calls in HEB-25 were fixed in BC1S3:8 generation, either toward the wild allele (19.9%) or the cultivated allele (28.8%). Most fixed SNP loci turned out to represent gene loci involved in domestication and flowering time as well as plant height, for example, btr1/btr2, thresh-1, Ppd-H1, and sdw1. Interestingly, also unknown loci were found where the exotic allele was fixed, hinting at potentially useful exotic alleles for plant breeding.

Dynamic Diversity of NLR Genes in Triticum and Mining of Promising NLR Alleles for Disease Resistance

Bread wheat is an essential crop with the second-highest global production after maize. Currently, wheat diseases are a serious threat to wheat production. Therefore, efficient breeding for disease resistance is extremely urgent in modern wheat. Here, we identified 2012 NLR genes from hexaploid wheat, and Ks values of paired syntenic NLRs showed a significant peak at 3.1–6.3 MYA, which exactly coincided with the first hybridization event between A and B genome lineages at ~5.5 MYA. We provided a landscape of dynamic diversity of NLRs from Triticum and Aegilops and found that NLR genes have higher diversity in wild progenitors and relatives. Further, most NLRs had opposite diversity patterns between genic and 2 Kb-promoter regions, which might respectively link sub/neofunctionalization and loss of duplicated NLR genes. Additionally, we identified an alien introgression of chromosome 4A in tetraploid emmer wheat, which was similar to that in hexaploid wheat. Transcriptome data from four experiments of wheat disease resistance helped to profile the expression pattern of NLR genes and identified promising NLRs involved in broad-spectrum disease resistance. Our study provided insights into the diversity evolution of NLR genes and identified beneficial NLRs to deploy into modern wheat in future wheat disease-resistance breeding.

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.

Pastoralism in Africa

To find the origins of African pastoralism it is important archaeologists look for the wild progenitors of animals. The wild sheep of Africa (Ammotragus lervia) were never domesticated, so all domestic sheep and goats came from the Near East. There has been some debate over whether there was an independent domestication of African cattle, because wild cattle (Bos primigenius) remains have been found in the Nile Valley. Genetic evidence shows that the source of African domesticated cattle was the Levant, some 8,000 years ago. Cattle spread across the Sahara as the environment was conducive to pastoralism, being well watered at this time. This lasted until after 5000 bp when the Intertropical Convergence Zone (ITCZ) retreated and the Sahara dried up to its present condition. The tsetse barrier also retreated at this time, allowing pastoralists to move south into West Africa and, via the Ethiopian highlands, to East Africa, arriving c.4500 bp, although it took another 1,000 years for them to fully adapt to the grasslands of southern Kenya and Tanzania. Domestic stock then went on to southern Africa via a tsetse-free corridor, arriving around 2000 bp. The effect of herding societies on local hunters throughout Africa appears to have been an initial rapprochement, with a later hardening of relations. In East Africa, this was probably due to the need to learn about the new environment with the help of local hunters and to adjust to new epizootic diseases. In southern Africa, the first pastoralists were primarily sheep herders during the 1st millennium bce, with few cattle bones being found from this time. Pastoralists only became fully fledged cattle herdsmen around 1000 bp when they developed the attributes of the historic Khoekhoen. A further debate existed in southern Africa over whether pastoralism there was the result of immigrant herders who arrived in the northern Kalahari and then spread to the Cape, or if local hunters took up sheep herding.

Inheritance of Qualitative Morphological Traits and Variation of Quantitative Agronomic Traits of Enset (Ensete Ventricosum (Welw.) Cheesman) Clones Obtained From Wolaita Zone, Southern Ethiopia

The present cultivated enset clonal landraces in Ethiopia originated from few wild progenitors. However, enset has a mixed mode of reproduction in which, the wild enset reproduces sexually through seeds, while cultivated enset is generally propagated vegetatively. The objective of this study was to understand the genetic structures of enset cultivars and estimate their genetic variability by evaluating the morphological data generated from progenies of cultivated and wild enset clones. Hence, seeds collected from six cultivated and four wild enset genotypes were used for this study. Data on four qualitative and six quantitative morphological traits were recorded from the progenies of the 10 enset genotypes. Progenies of seven enset genotypes segregated with 3:1 genetic ratio while progenies of the remaining genotypes segregated differently for the qualitative traits considered. With regard to the quantitative traits, the progenies of the 10 enset genotypes differed significantly for five of the six traits except pseudostem length. Generally the cultivated clones performed better than the wild types. This study demonstrated the possibility of creating genetic variation through selfing of the existing clones of enset for traits of interest and makes improvements either through selection or crossing the elite types to develop novel cultivar