Pollen tube growth and self-incompatibility in three Ziziphus species (Rhamnaceae)

Self-incompatibility and synchronous protandrous dichogamy have previously been reported in Ziziphus species. In this work, we conducted a comparative analysis of fluorescence microscopy observations of pollen tube growth following controlled cross pollinations of emasculated flowers and self-pollinations of non-emasculated flowers in three Ziziphus species, Z. jujuba, Z. mauritiana and Z. spina-christi, with the aim to determine the type of the self-incompatibility system of each species. In addition, to test whether autonomous self-pollination, parthenocarpy or agamospermy occurs, flowers were emasculated (or not) and covered. Fruit set and seed viability were monitored. The presence of binucleate pollen grains and the cessation of pollen tube growth in the style suggest that the self-incompatibility system operating in the studied Ziziphus species is gametophytically controlled. Controlled self-pollination in Z. mauritiana resulted in fruits that dropped off before maturation, whereas in Z. spina-christi the flowers dropped off one or two days after pollination. Following controlled self-pollination, small fruits lacking viable seeds were obtained in Z. jujuba, probably due to the stimulus provided by pollination (stimulative parthenocarpy). In the cultivar Tamar of Z. jujuba, the relatively high percentage of seedless fruits obtained in emasculated bagged flowers without hand pollination suggests that this cultivar can set seedless fruits without any pollination stimulus.     

Assessment of Genetic Diversity in Ziziphus mauritiana Using Inter-Simple Sequence Repeat Markers

Genetic diversity among 47 ber accessions belonging to cultivated species (Ziziphus mauritiana Lam) and one wild accession of Ziziphus nummularia (Burm F) Willed was investigated using Inter-Simple Sequence Repeat (ISSR) markers. A total of 167 amplification products were detected with 18 ISSR primers of which 152 (89.96%) were polymorphic. Most of the primers that produced distinct bands (14 primers out of 18) contained dinucleotide repeats. Primers based on (AC)n and (AG)_n repeats produced more polymorphic bands. Genetic similarity ranging from 43.07% to 90.30% suggested that the 48 Ziziphus genotypes used in the study were divergent. Cluster analysis based on UPGMA method and Bootstrap analysis separated all the 48 genotypes in four distinct clusters. The present study has successfully distinguished morphologically similar genotypes that emphasize the use of molecular markers to the taxonomists. Morphologically similar but genetically distinct genotypes, identified using ISSR markers could be potential sources for genotype identification and to resolve controversies over misnomination of ber genotypes. Present study is the first report on the exploitation of ISSR markers in ber for genetic diversity analysis.     

Diversity and relationships of Crocus sativus and its relatives analysed by inter-retroelement amplified polymorphism (IRAP)

Background and Aims: Saffron (Crocus sativus) is a sterile triploid (2n = 3x = 24) cultivated species, of unknown origin from other diploid and polyploid species in the genus Crocus (Iridaceae). Species in the genus have high morphological diversity, with no clear phylogenetic patterns below the level of section Crocus series Crocus. Using DNA markers, this study aimed to examine the diversity and relationships within and between species of Crocus series Crocus.Methods: Eleven inter-retroelement amplified polymorphism (IRAP) primers were used in 63 different combinations with 35 single-plant accessions of C. sativus and related Crocus species in order to determine genetic variability and to conduct phylogenetic analysis.Key Results: A total of 4521 distinct polymorphic bands from 100 bp to approx. 4 kb were amplified; no fragment specific to all accessions of a single species was amplified. The polymorphic information content (PIC) values varied from approx. 0·37 to approx. 0·05 (mean 0·17 ± 0·1) and the major allele frequency had a mean of 0·87. High levels of polymorphism were identified between accessions of the six species of Crocus series Crocus related to C. sativus, with further variation between the species. In contrast, no polymorphisms were seen among 17 C. sativus accessions obtained in the region from Kashmir through Iran to Spain.Conclusions In contrast to the intraspecific variability seen in other Crocus species, C. sativus has minimal genetic variation, and it is concluded that the triploid hybrid species has most probably arisen only once. The data show that saffron is an allotriploid species, with the IRAP analysis indicating that the most likely ancestors are C. cartwrightianus and C. pallasii subsp. pallasii (or close relatives). The results may facilitate resynthesizing saffron with improved characteristics, and show the need for conservation and collection of wild Crocus.     

Biological control of Ziziphus mauritiana (Rhamnaceae): feasibility,prospective agents and research gaps

The tropical fruit tree, Ziziphus mauritiana (Rhamnaceae), a native of the Indian subcontinent, is a pasture and environmental weed in northern Australia and Fiji. In their native range, Ziziphus spp., including commercially cultivated Z. mauritiana and Z. jujuba, are subjected to a wide range of pests and diseases. The feasibility of classical biological control of this weed has not been explored to date. Effective biological control could reduce plant vigour and seed output, thereby limiting the spread of Z. mauritiana in Australia. Two Ziziphus species are native to Australia, hence, any prospective biological control agent should be specific to Z. mauritiana. Opportunistic field surveys and literature searches identified 133 species of phytophagous insects, 9 species of phytophagous mites and 12 plant pathogens on Ziziphus spp. Host records suggest the following are possibly specific to Z. mauritiana and hence are prospective biological control agents in Australia: the seed‐feeding weevil Aubeus himalayanus; the leaf‐feeding gracillariid moth Phyllonorycter iochrysis; the leaf‐mining chrysomelid beetle Platypria erinaceus; the leaf‐folding crambid moth Synclera univocalis; the leaf‐galling midge Phyllodiplosis jujubae; and the gall‐mites Aceria cernuus and Larvacarus transitans. Host range of the rust Phakopsora zizyphi‐vulgaris includes many Ziziphus species, including the native Z. oenoplia and hence would not be a suitable biological control agent in Australia. The powdery mildew Pseudoidium ziziphi, with a host range restricted to Ziziphus species, has not been reported on Z. oenoplia. All available information on the pests and diseases of Z. mauritiana are from cultivated varieties. Hence, future surveys should focus on wild Z. mauritiana in the Indian subcontinent in areas that are climatically similar to the regions of northern Australia, where it is currently most abundant.     

Rapid SNP Discovery and a RAD-Based High-Density Linkage Map in Jujube (Ziziphus Mill.)

Background

Ziziphus Mill. (jujube), the most valued genus of Rhamnaceae, comprises of a number of economically and ecologically important species such as Z. jujuba Mill., Z. acidojujuba Cheng et Liu and Z. mauritiana Lam. Single nucleotide polymorphism (SNP) markers and a high-density genetic map are of great benefit to the improvement of the crop, mapping quantitative trait loci (QTL) and analyzing genome structure. However, such a high-density map is still absent in the genus Ziziphus and even the family Rhamnaceae. The recently developed restriction-site associated DNA (RAD) marker has been proven to be most powerful in genetic map construction. The objective of this study was to construct a high-density linkage map using the RAD tags generated by next generation sequencing.

Results

An interspecific F1 population and their parents (Z. jujuba Mill. ‘JMS2’ × Z. acidojujuba Cheng et Liu ‘Xing 16’) were genotyped using a mapping-by-sequencing approach, to generate RAD-based SNP markers. A total of 42,784 putative high quality SNPs were identified between the parents and 2,872 high-quality RAD markers were grouped in genetic maps. Of the 2,872 RAD markers, 1,307 were linked to the female genetic map, 1,336 to the male map, and 2,748 to the integrated map spanning 913.87 centi-morgans (cM) with an average marker interval of 0.34 cM. The integrated map contained 12 linkage groups (LGs), consistent with the haploid chromosome number of the two parents.

Conclusion

We first generated a high-density genetic linkage map with 2,748 RAD markers for jujube and a large number of SNPs were also developed. It provides a useful tool for both marker-assisted breeding and a variety of genome investigations in jujube, such as sequence assembly, gene localization, QTL detection and genome structure comparison.     

Morphological,phytochemical and genetic diversity of threatened Polygonatum verticillatum (L.) All. populations of different altitudes and habitat types in Himalayan region

Polygonatum verticillatum (L.) All. is an important medicinal herb that belongs to the family Asparagaceae. The rhizome of the species is used in Chyavanprash preparation and several other ayurvedic formulations. Numerous active constituents like saponins, alkaloids, phytohormones, flavonoids, antioxidants, lysine, serine, aspartic acid, diosgenin, β-sitosterol, etc. have been reported from this species. In this study, morphological, phytochemical, antioxidant and genetic variations of 11 distant populations of P. verticillatum were measured. Considerably (P < 0.05) higher variations were recorded among different populations of P. verticillatum using morphological, phytochemical and genetic diversity parameters. AGFW (above ground fresh weights); flavonols, FRAP (Ferric ion reducing antioxidant power) and NO (Nitric Oxide scavenging activity) were recorded maximum in Kafni population. Similarly, a significantly higher above and below ground dry weight was recorded in Mayawati and Surmoli populations respectively. Maximum phenolic content, tannins, and DPPH (2,2-diphenyl-1-picrylhydrazyl) activity were recorded in Milam population. A total of 165 individuals from 11 populations were assessed for genetic diversity using inter-simple sequence repeats (ISSR) marker. High genetic diversity (He = 0.35) was recorded in Himkhola and Surmoli populations while it was observed minimum (0.28) in the Mayawati population. Altitude showed a significant positive correlation with tannins (r = 0.674; P < 005) and DPPH (r = 0.820; P < 0.01). Phenol content exhibited a considerably positive relationship with He (r = 0.606; P < 0.05) and BGFW (r = 0.620; P < 0.05), flavonol displayed a positive correlation with Pp% (r = 0.606; P < 0.05). The population structure of P. verticillatum, exhibited that the optimal value of the K was 3 for its populations as determined by the ΔK statistic structure. Among populations, the amount of gene flow is higher (Nm = 1.717) among all sites. Hence, it can be concluded that P. verticillatum populations possess considerable variability in the collected populations. Likewise, the populations from Kafni, Satbunga and Himkhola with higher morphological, phytochemicals and genetic variability were prioritized and therefore recommended for cultivation and mass multiplication to meet the industrial demand for target species.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01044-9.     

Genetic diversity of Indian jujube cultivars using SCoT,ISSR, and rDNA markers

Genetic variation and relationships among 37 cultivars of Ziziphus mauritiana (Lamk.) native of India were analyzed using start codon targeted (SCoT), inter-simple sequence repeats (ISSR), and ribosomal DNA (rDNA) markers. High level of polymorphism among SCoT (61.6%) and ISSR (61%) primers with higher PIC values ranging from 63.1 to 90.4% of SCoT and 47.3 to 88.8% of ISSR primers was recorded. SCoT and ISSR dendrograms revealed similarity coefficients ranging from 0.80 to 0.92 and 0.79 to 0.96, respectively, and clearly delineated all the cultivars of Z. mauritiana into well-supported distinct clusters. Greater Gst signifies higher amount of differentiation observed over multiple loci among seven Z. mauritiana populations. On the other hand, higher gene flow demonstrating a very high migration rate between Z. mauritiana populations indicated higher rates of transfer of alleles or genes from one population to another. The genetic diversity of population 1 (Rajasthan) was the richest among all the seven populations. The largest genetic distance was measured between Maharashtra and West Bengal and the least between Rajasthan and Punjab cultivars. Most of the genetic diversity exists within population rather than among populations. Substantial variation in the ITS-1 region signifies its phylogenetic utility specifically in assessing genetic diversity in Z. mauritiana. The clustering patterns using three molecular marker systems vis-à-vis place of origin exhibited no consistency in grouping of Z. mauritiana cultivars as cultivars from the same place of origin were genetically cataloged into different SCoT, ISSR, and ITS phylogram clusters indicating wide genetic diversity and distribution across agro-climatic zones validating the robustness of marker systems tested.     

Exploring genetic variations in threatened medicinal orchids using start codon targeted (SCoT) polymorphism and marker-association with seed morphometric traits

We aimed to study the genetic diversity and population structure of eight Iranian terrestrial orchid species, including Anacamptis coriophora (L.) R. M. Bateman, Pridgeon and M. W. Chase, Dactylorhiza umbrosa (Kar. & Kir.) Nevski, Himantoglossum affine (Boiss.) Schltr., Orchis collina Banks and Solander, Orchis mascula (L.) L., Orchis simia Lam., Ophrys schulzei Bornm. and Fleischm., and Ophrys straussii H. Fleischm. and Bornm. using start target codon markers (SCoT) and finding markers associated with seed morphometric traits. A total of 254 reproducible SCoT fragments were generated, of which 248 fragments were polymorphic (average polymorphism of 96.18%). The SCoT markers showed a narrow range of polymorphism information content (PIC) varied from 0.397 for S9 primer to 0.499 for S11 and S20 primers. Based on the population analysis results, the Orchis simia accessions collected from Paveh region (Os.P) represented the lowest observed number of alleles (Na) (1.13) and effective number of alleles (Ne) (1.09). At the same time, the highest Na (1.29) and Ne (1.18) values were obtained in O. schulzei collected from Javanrood (Oyst.JA). Shannon’s information index (I) was ranged from 0.03 for D. umbrosa accessions collected from Marivan (Du.M population) to 0.263 for Ha.Ja population (H. affine accessions collected from Javanrood). The UPGMA dendrogram obtained with the Jaccard similarity coefficient (r = 0.97295) divided 97 studied terrestrial orchid accessions into eight groups mainly based on species type and geographical origin. Based on the Bayesian statistical index, the highest probability of the data was achieved when accessions were divided into eight groups (K = 8). Multiple association analysis (MRA) revealed significant associations between some of SCoT bands with seed morphometric traits. Our findings can be useful for germplasm characterization, conservation, and improvement of Iranian terrestrial orchid species.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-00978-4.     

Field comparisons of photosynthesis and leaf conductance in Ziziphus mauritiana and other fruit tree species in Zimbabwe

 Data are presented for gas exchange in exposed leaves in field grown Ziziphus mauritiana (Lamk.) at a highland site and potted seedlings at a hotter lowland site in tropical Zimbabwe, together with indigenous and locally-grown commercial fruit crops. The field trial at the highland site included local Ziziphus mauritiana, introduced Indian Z. mauritiana (cv. Umran), fig and peach. In all species assimilation was highest early in the morning, followed by a gradual decline throughout the remainder of the day. Leaf conductance followed the same trend as assimilation for fig and peach, but in Ziziphus cv. Umran and Ziziphus Musau, conductance tracked irradiance, reaching a maximum in the middle of the day. In all species, sub-stomatal CO₂ concentrations increased with declining assimilation indicating that during high irradiance, assimilation was mainly controlled by mesophyll limitations rather than conductance. At the highland site both Ziziphus cv. Umran and Musau were highly productive, with light saturated assimilation significantly higher than in either fig or peach (P < 0.01). At the warmer lowland site, assimilation and conductance in Ziziphus Musau were also higher than in other indigenous fruit tree species growing under similar conditions. Despite increased assimilation in Ziziphus, when compared to the other species, there was no increase in the assimilation ratio (ratio of assimilation/conductance) which was offset by the high conductance values. The data indicate that under conditions where water was not limiting, young Ziziphus showed no enhanced stomatal control over water loss, but was highly productive (per unit leaf area) relative to the other species. Received: 17 October 1996 / Accepted: 8 January 1997     

New approach for determination of an optimum honeybee colony’s carrying capacity based on productivity and nectar secretion potential of bee forage species

The present study was carried out to determine an optimum honeybee colony’s carrying capacity of selected valleys dominated by Ziziphus spina-christi and Acacia tortilis in the Al-Baha region, Kingdom of Saudi Arabia. The study was conducted based on the assessment of the number of colonies kept, their productivities and the existing productive bee forage resources in the target valleys with its economic implication. In the existing beekeeping practice, the average number of managed honeybee colonies introduced per square kilometer was 530 and 317 during the flowering period of Z. spina-christi and A. tortilis, respectively. Furthermore, the overall ratios of productive bee forage plants to the number of honeybee colonies introduced were 0.55 and 11.12 to Ziziphus trees and A. tortilis shrubs respectively. In the existing situation the average honey production potential of 5.21 and 0.34 kg was recorded per Ziziphus and A. tortilis plants per flowering season, respectively. The present study, revealed that the number of honeybee colonies introduced in relation to the existing bee forage potential was extremely overcrowding which is beyond the carrying capacity of bee forage resources in selected valleys and it has been observed to affect the productivities and subsequent profitability of beekeeping. The study infers that, by keeping the optimum honeybee colony’s carrying capacity of valleys (88 traditional hives/km² or 54 Langstroth hives/km² in Ziziphus field and 72 traditional hives/km² or 44 Langstroth hives/km² in A. tortilis field), profitability of beekeeping can be boosted up to 130.39% and 207.98% during Z. spina-christi and A. tortilis, flowering seasons, respectively.     

Analysis of molecular genetic diversity in a representative collection of foxtail millet [Setaria italica (L.) P. Beauv.] from different agro-ecological regions of India

Foxtail millet [Setaria italica (L.) P. Beauv.], an important crop of East Asia is known for its drought tolerance and was once an indispensible crop of vast rainfed areas in semi-arid regions in India. In India it is cultivated in Andhra Pradesh, Karnataka, Maharashtra, Tamil Nadu, Rajasthan, Madhya Pradesh, Uttar Pradesh and north eastern states. The grain finds use in several local recipes such as roti (bread), jaula, singal, sirol. Foxtail millet grain contains 12.3 % protein, 4.7 % fat, 60.6 % carbohydrates, and 3.2 % ash. The present study was conducted to analyse the genetic diversity among foxtail accessions from different states of India and a few exotic accessions using RAPD and ISSR techniques and identify diverse accessions for use in variety improvement programmes. A set of 125 foxtail millet accessions selected from 11 different agro-ecological regions of India were analyzed using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) marker techniques. A total of 146 (115 RAPD and 31 ISSR) scoreable markers were generated with 16 RAPD and four ISSR primers. The dendrogram generated using Nei’s genetic distances and principal component analyses revealed presence of two clusters and two subclusters in group I. The accessions from Andhra Pradesh, Karnataka, Maharashtra and Uttarakhand were more diverse since they were distributed in both the clusters. There was no clear geographical differentiation observable. The bootstrap support for the major groups identified was strong (above 80 %) indicating good statistical support. The average value of Nei and Li’s genetic distance was lowest (0.081) for accessions from West Bengal while the collections from Karnataka showed highest dissimilarity (average genetic distance = 0.239). The average genetic distance for all 125 accessions together was 0.177 indicating presence of only moderate genetic diversity in the collections. The analysis of molecular variance indicated that only 2.76 % variation was explained by variations among the groups and 11.55 % among populations within groups. However the percentage of variation observed within populations was high (85.68). The value of Fst was observed to be very low (0.028) indicating low differentiation of the accessions analysed. The population genetic analysis carried out indicates that highest number of alleles per locus (1.745 ± 0.438) was observed for Andhra Pradesh with 35 accessions. When four eco-geographic regions were considered, the southern region comprising AP, Karnataka and TN showed the highest number of alleles per locus (1.787 ± 0.411). The value of Gst was lowest for south (0.123) and highest for central west (0.455). This indicated that all the landraces from south share common alleles. The gene flow between the accessions from different regions was also observed to be high with the highest migration (3.557) recorded for south.     

Genomic insight into the developmental history of southern highbush blueberry populations

Interspecific hybridization is a common breeding approach for introducing novel traits and genetic diversity to breeding populations. Southern highbush blueberry (SHB) is a blueberry cultivar group that has been intensively bred over the last 60 years. Specifically, it was developed by multiple interspecific crosses between northern highbush blueberry [NHB, Vaccinium corymbosum L. (2n = 4x = 48)] and low-chill Vaccinium species to expand the geographic limits of highbush blueberry production. In this study, we genotyped polyploid blueberries, including 105 SHB, 17 NHB, and 10 rabbiteye blueberry (RE) (Vaccinium virgatum Aiton), from the accessions planted at Poplarville, Mississippi, and accessions distributed in Japan, based on the double-digest restriction site-associated DNA sequencing. The genome-wide SNP data clearly indicated that RE cultivars were genetically distinct from SHB and NHB cultivars, whereas NHB and SHB were genetically indistinguishable. The population structure results appeared to reflect the differences in the allele selection strategies that breeders used for developing germplasm adapted to local climates. The genotype data implied that there are no or very few genomic segments that were commonly introgressed from low-chill Vaccinium species to the SHB genome. Principal component analysis-based outlier detection analysis found a few loci associated with a variable that could partially differentiate NHB and SHB. These SNP loci were detected in Mb-scale haplotype blocks and may be close to the functional genes related to SHB development. Collectively, the data generated in this study suggest a polygenic adaptation of SHB to the southern climate, and may be relevant for future population-scale genome-wide analyses of blueberry.Subject terms: Agricultural genetics, Plant breeding     

SNP detection and population structure evaluation of Salix gordejevii Y. L. Chang et Skv. in Hunshandake Sandland,Inner Mongolia,China

Single nucleotide polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism and, hence, are highly favorable markers for genetic map construction and genome-wide association studies. Based on the DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection, the genetic diversity and population structure of Salix gordejevii Y. L. Chang et Skv., a valuable sand-fixing shrub, was assessed in 199 accessions from 20 populations in Hunshandake Sandland of northern China. A total of 623.15 M reads resulted in 30.49 × sequencing depth on average and a mean Q30 of 95.70%, and 2,287,715 SNPs in 178,509 polymorphic SLAF tags were obtained. By discarding minor allele frequency > 0.05 and integrity > 0.8, a total of 93,600 SNPs were retained for population genetic analyses, which revealed that 199 individuals could be divided into six groups based on cross-validation errors. However, this grouping pattern did not match the geographical distribution, indicating that there is no apparent geographic barrier in the blank areas where S. gordejevii was not distributed in Hunshandake Sandland. In addition, the physical distance of linkage disequilibrium decay in the analyzed S. gordejevii individuals was 18.5 kb when r² = 0.1. The linkage disequilibrium decay distances for different chromosomes varied from 4.6 kb (chromosome 16) to 37.8 kb (chromosome 3). The obtained SNPs offer suitable marker resources for further genetic and genomic studies and will benefit S. gordejevii breeding programs.     

Assessment of the Genetic Diversity of Different Job's Tears (Coix lacryma-jobi L.) Accessions and the Active Composition and Anticancer Effect of Its Seed Oil

Job’s tears (Coix lachryma-jobi L.) is an important crop used as food and herbal medicine in Asian countries. A drug made of Job’s tears seed oil has been clinically applied to treat multiple cancers. In this study, the genetic diversity of Job’s tears accessions and the fatty acid composition, triglyceride composition, and anti-proliferative effect of Job’s tears seed oil were analyzed using morphological characteristics and ISSR markers, GC-MS, HPLC-ELSD, and the MTT method. ISSR analysis demonstrated low genetic diversity of Job’s tears at the species level (h = 0.21, I = 0.33) and the accession level (h = 0.07, I = 0.10), and strong genetic differentiation (G_ST = 0.6702) among all accessions. It also clustered the 11 accessions into three cultivated clades corresponding with geographical locations and two evidently divergent wild clades. The grouping patterns based on morphological characteristics and chemical profiles were in accordance with those clustered by ISSR analysis. Significant differences in morphological characteristics, fatty acid composition, triglyceride composition, and inhibition rates of seed oil were detected among different accessions, which showed a highly significant positive correlation with genetic variation. These results suggest that the seed morphological characteristics, fatty acid composition, and triglyceride composition may be mainly attributed to genetic factors. The proportion of palmitic acid and linoleic acid to oleic acid displayed a highly significant positive correlation with the inhibition rates of Job’s tears seed oil for T24 cells, and thus can be an important indicator for quality control for Job’s tears.     

Population genomics and conservation management of a declining tropical rodent

Conservation management is improved by incorporating information about the spatial distribution of population genetic diversity into planning strategies. Northern Australia is the location of some of the world’s most severe ongoing declines of endemic mammal species, yet we have little genetic information from this regional mammal assemblage to inform a genetic perspective on conservation assessment and planning. We used next-generation sequencing data from remnant populations of the threatened brush-tailed rabbit-rat (Conilurus penicillatus) to compare patterns of genomic diversity and differentiation across the landscape and investigate standardised hierarchical genomic diversity metrics to better understand brush-tailed rabbit-rat population genomic structure. We found strong population structuring, with high levels of differentiation between populations (F_ST = 0.21–0.78). Two distinct genomic lineages between the Tiwi Islands and mainland are also present. Prioritisation analysis showed that one population in both lineages would need to be conserved to retain at least ~80% of alleles for the species. Analysis of standardised genomic diversity metrics showed that approximately half of the total diversity occurs among lineages (δ = 0.091 from grand total γ = 0.184). We suggest that a focus on conserving remnant island populations may not be appropriate for the preservation of species-level genomic diversity and adaptive potential, as these populations represent a small component of the total diversity and a narrow subset of the environmental conditions in which the species occurs. We also highlight the importance of considering both genomic and ecological differentiation between source and receiving populations when considering translocations for conservation purposes.Subject terms: Ecological genetics, Population genetics, Conservation biology, Biogeography     

Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus

Background

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation. Identification of large numbers of SNPs is helpful for genetic diversity analysis, map-based cloning, genome-wide association analyses and marker-assisted breeding. Recently, identifying genome-wide SNPs in allopolyploid Brassica napus (rapeseed, canola) by resequencing many accessions has become feasible, due to the availability of reference genomes of Brassica rapa (2n = AA) and Brassica oleracea (2n = CC), which are the progenitor species of B. napus (2n = AACC). Although many SNPs in B. napus have been released, the objective in the present study was to produce a larger, more informative set of SNPs for large-scale and efficient genotypic screening. Hence, short-read genome sequencing was conducted on ten elite B. napus accessions for SNP discovery. A subset of these SNPs was randomly selected for sequence validation and for genotyping efficiency testing using the Illumina GoldenGate assay.

Results

A total of 892,536 bi-allelic SNPs were discovered throughout the B. napus genome. A total of 36,458 putative amino acid variants were located in 13,552 protein-coding genes, which were predicted to have enriched binding and catalytic activity as a result. Using the GoldenGate genotyping platform, 94 of 96 SNPs sampled could effectively distinguish genotypes of 130 lines from two mapping populations, with an average call rate of 92%.

Conclusions

Despite the polyploid nature of B. napus, nearly 900,000 simple SNPs were identified by whole genome resequencing. These SNPs were predicted to be effective in high-throughput genotyping assays (51% polymorphic SNPs, 92% average call rate using the GoldenGate assay, leading to an estimated >450 000 useful SNPs). Hence, the development of a much larger genotyping array of informative SNPs is feasible. SNPs identified in this study to cause non-synonymous amino acid substitutions can also be utilized to directly identify causal genes in association studies.     

Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry

Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (Fragaria chiloensis and Fragaria virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication—59–76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that F. × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8 M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis,F. virginiana, and F. × ananassa (π = 0.0059–0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern F. × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.     

Uncovering the genetic diversity of yams (Dioscorea spp.) in China by combining phenotypic trait and molecular marker analyses

Yam is an important edible tuber and root plant worldwide; China as one of the native places of yams has many diverse local resources. The goal of this study was to clarify the genetic diversity of the commonly cultivated yam landraces and the genetic relationship between the main yam species in China. In this study, 26 phenotypic traits of 112 yam accessions from 21 provinces in China were evaluated, and 24 simple sequence repeat (SSR) and 29 sequence‐related amplified polymorphism (SRAP) markers were used for the genetic diversity analysis. Phenotypic traits revealed that Dioscorea opposita had the highest genetic diversity, followed by D. alata, D. persimilis, D. fordii, and D. esculenta. Among the 26 phenotypic traits, the Shannon diversity indexes of leaf shape, petiole color, and stem color were high, and the range in the variation of tuber‐related traits in the underground part was higher than that in the aboveground part. All accessions were divided into six groups by phenotypic trait clustering, which was also supported by principal component analysis (PCA). Molecular marker analysis showed that SSR and SRAP markers had good amplification effects and could effectively and accurately evaluate the genetic variation of yam. The unweighted pair‐group method with arithmetic means analysis based on SSR‐SRAP marker data showed that the 112 accessions were also divided into six groups, similar to the phenotypic trait results. The results of PCA and population structure analysis based on SSR‐SRAP data also produced similar results. In addition, the analysis of the origin and genetic relationship of yam indicated that the species D. opposita may have originated from China. These results demonstrate the genetic diversity and distinctness among the widely cultivated species of Chinese yam and provide a theoretical reference for the classification, breeding, germplasm innovation, utilization, and variety protection of Chinese yam resources.     

Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation across Africa

Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (H_E = 0.833) to the modern (H_E = 0.796) populations, whereas mitochondrial genetic diversity was maintained (H_d = 0.98 for both). Although the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified four clusters: Southern, Mixed, Eastern, and Western and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, whereas mitochondrial structure and diversity were maintained over time.