Wild Germplasm Research Articles

Core Collection Formation in Guatemalan Wild Avocado Germplasm with Phenotypic and SSR Data

Guatemala’s wild avocado germplasm holds vital genetic value, but lacking conservation strategies imperils it. Studying its diversity is pivotal for conservation and breeding. The study aimed to comprehensively assess the wild avocado germplasm in Guatemala by combining phenotypic and genotypic data and to create a core collection for conservation and future breeding programs. A total of 189 mature avocado trees were sampled across Guatemala’s northern, southern, and western regions. Morphological characteristics were documented, and genetic diversity was assessed using 12 SSR loci. The investigated germplasm revealed three distinct genetic clusters, exhibiting an average gene diversity of 0.796 and a 7.74% molecular variation among them. The samples showed various morphological characteristics that indicate the presence of three avocado races in Guatemala. The weak correlation between phenotypic and genotypic distances highlighted their independence and complementary nature. The joint matrix effectively integrated and captured genotypic and phenotypic data for comprehensive genetic diversity analysis. A core collection comprising 20% of total accessions that captured maximum genetic diversity was formed. This study exposed wild Guatemalan avocados’ genetic diversity, morphological traits, and conservation significance. Integrated data capture via clustering validates holistic genetic insight for conservation and breeding strategies.

Allele mining of eukaryotic translation initiation factor genes in Prunus for the identification of new sources of resistance to sharka

Members of the eukaryotic translation initiation complex are co-opted in viral infection, leading to susceptibility in many crop species, including stone fruit trees (Prunus spp.). Therefore, modification of one of those eukaryotic translation initiation factors or changes in their gene expression may result in resistance. We searched the crop and wild Prunus germplasm from the Armeniaca and Amygdalus taxonomic sections for allelic variants in the eIF4E and eIFiso4E genes, to identify alleles potentially linked to resistance to Plum pox virus (PPV). Over one thousand stone fruit accessions (1397) were screened for variation in eIF4E and eIFiso4E transcript sequences which are in single copy within the diploid Prunus genome. We identified new alleles for both genes differing from haplotypes associated with PPV susceptible accessions. Overall, analyses showed that eIFiso4E is genetically more constrained since it displayed less polymorphism than eIF4E. We also demonstrated more variations at both loci in the related wild species than in crop species. As the eIFiso4E translation initiation factor was identified as indispensable for PPV infection, a selection of ten different eIFiso4E haplotypes along 13 accessions were tested by infection with PPV and eight of them displayed a range of reduced susceptibility to resistance, indicating new potential sources of resistance to sharka.

Genome-wide profiling of genetic variations reveals the molecular basis of aluminum stress adaptation in Tibetan wild barley

Aluminum (Al) toxicity in acidic soil is a major factor affecting crop productivity. The extensive genetic diversity found in Tibetan wild barley germplasms offers a valuable reservoir of alleles associated with aluminum tolerance. Here, resequencing of two Al-tolerant barley genotypes (Tibetan wild barley accession XZ16 and cultivated barley Dayton) identified a total of 19,826,182 and 16,287,277 single nucleotide polymorphisms (SNPs), 1628,052 and 1386,973 insertions/deletions (InDels), 61,532 and 57,937 structural variations (SVs), 248,768 and 240,723 copy number variations (CNVs) in XZ16 and Dayton, respectively, and uncovered approximately 600 genes highly related to Al tolerance in barley. Comparative genomic analyses unveiled 71 key genes that contain unique genetic variants in XZ16 and are predominantly associated with organic acid exudation, Al sequestration, auxin response, and transcriptional regulation. Manipulation of these key genes at the genetic and transcriptional level is a promising strategy for developing optimal haplotype combinations and new barley cultivars with improved Al tolerance. This study represents the first comprehensive examination of genetic variation in Al-tolerant Tibetan wild barley through genome-wide profiling. The obtained results make the deep insight into the mechanisms underlying barley adaptation to Al toxicity, and identified the candidate genes useful for improvement of Al tolerance in barley.

Development of genomic SSR markers for characterization of genetic diversity in wild pomegranate germplasm

Development of genomic SSR markers for characterization of genetic diversity in wild pomegranate germplasm

A multiplexed plant-animal SNP array for selective breeding and species conservation applications.

Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant-animal single nucleotide polymorphism array, including both closely and distantly related species, was explored. The performance of the single nucleotide polymorphism array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the single nucleotide polymorphism array as a technique to further reduce costs was evaluated. Single nucleotide polymorphism performance was generally high, and species-specific single nucleotide polymorphisms proved suitable for diverse applications. The multi-species single nucleotide polymorphism array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.

Comparative transcriptome profiling to unravel the key molecular signalling pathways and drought adaptive plasticity in shoot borne root system of sugarcane

Sugarcane root system comprises of superficial sett roots as well as deeply-penetrating shoot borne roots (SBR) with latter being the permanent root system. In sugarcane, the healthy SBR contributes to a better crop yield and it also helps to produce multiple ratoon crops after the harvest. There is a dearth of in-depth knowledge on SBR system architecture and its functional role in modern day commercial hybrids. A comprehensive phenotypic, anatomical and whole transcriptome profiling, conducted between the commercial sugarcane hybrids and a wild germplasm Erianthus, found a developmental delay in both initiation and establishment of the SBR in commercial hybrid compared to Erianthus. The SBR system in Erianthus proved to be an extensive drought-adaptive root system architecture that significantly contributes to drought tolerance. On the other hand, SBRs in the commercial hybrids showed an irreversible collapse and damage of the root cells under drought stress. The outcomes from the comparative analysis of the transcriptome data showed a significant upregulation of the genes that regulate important stress signalling pathways viz., sugar, calcium, hormone signalling and phenylpropanoid biosynthesis in the SBRs of Erianthus. It was found that through these key signalling pathways, Erianthus SBRs triggered the downstream signalling cascade to impart physiological responses like osmoprotection, modification of the cell walls, detoxification of reactive oxygen species, expression of drought responsive transcription factors, maintenance of cell stability and lateral root development. The current study forms a basis for further exploration of the Shoot Borne Root system as a valuable breeding target to develop drought tolerant sugarcane genotypes.

Exploring seed and meal composition and protein solubility in soybean genotypes from different domestication periods

AbstractTraditionally, commercial soybean breeding has focused on increasing seed yield by crossing elite cultivars and limiting the genetic diversity within commercial germplasm. Wild and ancestral soybean genotypes have higher seed protein concentrations than commercial ones. Different seed protein concentrations and compositions result in diverse functional properties of soybean meal, in particular solubility is important for beverages and protein isolates production. The objectives of our study were (i) to characterize seed protein concentration and composition in genotypes from different soybean domestication periods (types) and (ii) to evaluate the protein concentration and solubility profiles of the defatted meals obtained from these genotypes. Variation within seed and meal protein concentration, composition, and solubility was evident along the domestication process. Wild relative (G. soja) and Elite genotypes had the maximum and minimum seed protein concentrations, respectively (42.9 and 36.3 g 100 g−1). Soybean meal protein concentrations were 55.1, 47.7, 48.4 and 44.1 g 100 g−1 for Wild relative (G. soja), Asian landraces, North American (Nam) ancestors and Elite, respectively. Ample genotypic variation was observed for β‐conglycinin components, such as for β, α, and α′ subunits and for total glycinin and its components. Asian landraces had the highest protein solubility. Wild and ancestral germplasm are a reservoir of useful traits to improve soybean seed quality. This study opens the gates to the introduction of ancestral germplasm to breeding programs focused on protein quality and functionality.

Waterlogging Tolerance of Actinidia valvata Dunn Is Associated with High Activities of Pyruvate Decarboxylase, Alcohol Dehydrogenase and Antioxidant Enzymes.

Kiwifruit (Actinidia spp.) is susceptible to waterlogging stress. Although abundant wild germplasm resources exist among Actinidia plants for improving the waterlogging tolerance of kiwifruit cultivars, the underlying mechanisms remain largely unknown. Here, a comparative study was undertaken using one wild germplasm, Maorenshen (A. valvata Dunn, MRS), and one cultivar, Miliang-1 (A. chinensis var. deliciosa (A.Chev.) A.Chev. cv. Miliang-1, ML). Under stress, the ML plantlets were seriously damaged with wilted chlorotic leaves and blackened rotten roots, whereas the symptoms of injury in the MRS plantlets were much fewer, along with higher photosynthetic rates, chlorophyll fluorescence characteristics and root activity under stress conditions. However, neither aerenchyma in the root nor adventitious roots appeared in both germplasms upon stress exposure. The activities of pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH), as well as their transcript levels, were constitutively higher in MRS than those in ML under both normal and stress conditions. Waterlogging stress significantly enhanced the PDC and ADH enzyme activities in both germplasms, which were 60.8% and 22.4% higher in the MRS roots than those in the ML roots under waterlogging stress, respectively. Moreover, MRS displayed higher activities of antioxidant enzymes, including SOD, CAT, and APX, as well as DPPH-radical scavenging ability, and decreased H2O2 and MDA accumulation under both normal and stress conditions. Our findings suggest that the waterlogging tolerance of the wild A. valvata germplasm was associated with high PDC and ADH, as well as antioxidant ability.

Construction of a Tomato (Solanum lycopersicum L.) Introgression Line Population and Mapping of Major Agronomic Quantitative Trait Loci

Tomato as a fresh fruit has a large market share in China, but few new materials have been developed for such cultivar breeding in recent years. This study aims to create innovative breeding materials for fresh fruit tomatoes with consistent genetic backgrounds and take advantage of beneficial genes from wild germplasm resources. An introgression line (IL) population was constructed using freshly cultivated tomato S. lycopersicum 1052 and wild tomato S. pennellii LA0716 through hybridization and five consecutive backcrossings, with molecular marker-assisted selection techniques during seedling stages. A total of 447 cleaved amplified polymorphic sequences (CAPS) and 525 simple sequence repeat (SSR) markers were used to screen polymorphic markers among the two parental lines, resulting in 216 polymorphic CAPS and 236 polymorphic SSR markers, with 46.5% parental polymorphism. Then, 200 molecular markers uniformly distributed over the entire genome were further selected, and 107 ILs were finally obtained from 541 BC5 candidate plants. The physical distance between adjacent markers was 6.3~10.0 cm, with an average interval of 7.29 cm, and the IL population constructed covered the whole genome of S. pennillii LA0716, with an average introgression segment of 31.5 cm. Moreover, phenotype data of major agronomic traits in BC5 progeny after selfing two times, were analyzed for quantitative trait locus (QTL) mapping, and a total of 11 QTLs distributed on 6 chromosomes were identified, including 3 QTLs regulating plant height, 1 QTL regulating leaf size, 1 QTL regulating fruit color, 4 QTLs regulating fruit weight, and 2 QTLs regulating soluble solids content in ripening fruits. The IL population constructed in this study provided good materials for fresh fruit tomato breeding with improved yield and quality in the future.

In Vitro Assessment of Salt Stress Tolerance in Wild Potato Species

Proof of concept salt tolerance and plasticity. Wild germplasm may represent a precious source of genetic variability for salt tolerance. This study evaluated the morphological changes occurring under controlled and saline conditions in tuber-bearing S. bulbocastanum, S. commersonii, S. chomatophyllum, S. multidissectum, S. pinnactisectum, S. phureja, and cultivated S. tuberosum. An in vitro screening method was employed. Significant phenotypic variations were observed for all phenotypic traits analyzed at all NaCl levels (0, 40, 60, and 120 mM). In addition, a significant correlation between root plasticity and salt tolerance was found. Further, changes in proline and total phenolic content were assessed to envisage the metabolic adjustments of tolerant clones towards salinity. The most promising sources of tolerance were identified in S. commersonii and S. multidissectum and information obtained is discussed from a breeding perspective.

Genetic Diversity of 52 Species of Kiwifruit (Actinidia chinensis Planch.)

The genetic diversity of 52 kiwifruit wild germplasms, which were collected by the kiwifruit germplasm nursery of the Guangxi Institute of Botany, was studied using start-codon-targeted (SCoT) molecular markers. The objective was to understand the genetic relationships of the 52 kiwifruit wild germplasms. The results showed that a total of 113 bands were amplified from 52 wild kiwifruit germplasms using 10 primers (9–17 bands per primer, 11.3 on average), of which 103 (91.15%) were polymorphic bands (10.3 bands per primer). The genetic identity of the 52 wild kiwifruit germplasms was in the range of 0.405–1.000, with an average of 0.709. The genetic distance was 0.000–0.904, with an average of 0.355. At the threshold of 0.650, the germplasms were clustered into three clusters. The genetic distances between Guilin and Fushekuoye and between Jinhua and Liangye were both the smallest (0.000), meaning they had a similarity of 100%, as indicated by the SCoT molecular markers. In conclusion, the genetic relationships at the molecular level (genetic distance) were clustered preferentially according to the place of origin instead of by morphological classification, geographical distribution, or ploidy. The genetic relationships between wild kiwifruit germplasms were partially verified through disease resistance analysis.

Genetic Variation in Tolerance to Iron Deficiency among Species of Oryza

Transplanted rice cultivation has caused groundwater depletion in several regions globally. Direct-seeded rice under aerobic conditions is a water-saving alternative. However, under aerobic conditions, iron in the soil is oxidized from the ferrous to ferric forms, which are not easily available to rice crops, resulting in iron-deficiency-induced chlorosis (IDIC) and causing significant reductions in yield. Cultivated rice accessions have limited variations in IDIC tolerance, while the wild Oryza germplasm could be a potential source of IDIC tolerance. In this study, 313 Oryza accessions were evaluated for IDIC tolerance at the tillering stage under aerobic conditions and 20 IDIC-tolerant lines were identified. The twenty lines showed no signs of chlorosis and had high levels of iron content and SPAD values, while the eight cultivated controls exhibited varying degrees of chlorosis symptoms and low levels of SPAD and iron content. To confirm their tolerance, the selected lines were evaluated again in a subsequent year, and they showed comparable levels of tolerance, indicating that these lines were efficient in iron uptake and utilization, resulting in maintained high chlorophyll and leaf area index. These accessions may be useful for developing IDIC-tolerant cultivars for aerobic rice cultivation and future studies of the molecular basis of IDIC tolerance.

Genome sequence analysis provides insights into the mode of 2n egg formation in Solanum malmeanum.

Our genomic investigation confirms the mechanism of 2n eggs formation in S. malmeanum and aid in optimizing the use of wild germplasm. Wild potatoes are a valuable source of agronomic traits. However, substantial reproductive barriers limit gene flow into cultivated species. 2n gametes are instrumental in preventing endosperm abortion caused by genetic imbalances in the endosperm. However, little is known about the molecular mechanisms underlying the formation of 2n gametes. Here, the wild species Solanum malmeanum Bitter (2x, 1EBN, endosperm balance number) was used in inter- and intrapoloid crosses with other Solanum species, with viable seeds being produced only when S. malmeanum was used as the female parent to cross the 2EBN Solanum genus and with the likely involvement of 2n gametes. Subsequently, we substantiated the formation of 2n eggs in S. malmeanum using fluorescence in situ hybridization (FISH) and genomic sequencing technology. Additionally, the transmission rate of maternal heterozygous polymorphism sites was assessed from a genomic perspective to analyze the mode of 2n egg formation in S. malmeanum × S. tuberosum and S. malmeanum × S. chacoense crosses; each cross acquired an average of 31.12% and 22.79% maternal sites, respectively. This confirmed that 2n egg formation in S. malmeanum attributed to second-division restitution (SDR) coupled with the occurrence of exchange events. The high-throughput sequencing technology used in this study has strong advantages over traditional cytological analyses. Furthermore, S. malmeanum, which has a variety of excellent traits not available from present cultivated potato genepool, has received little research attention and has successfully achieved gene flow in cultivated species in the current study. These findings will facilitate the understanding and optimization of wild germplasm utilization in potatoes.

Cyto-Embryological Analysis of Wild Kentucky Bluegrass Germplasm in Gansu Province, China

Reproduction studies, particularly embryology, represent basic information of any plant. However, the current embryological information is fragmentary for Kentucky bluegrass (Poa pratensis L.). Here, paraffin sections were used to examine the cyto-embryological characteristics, including microsporogenesis, microgametogenesis, megasporogenesis, megagametogenesis, and apomixis, of wild Kentucky bluegrass germplasm from Gannan (GN) and Longnan (LN) in Gansu Province. The study found no significant differences in pollen diameter, characteristics, viability, and stigma receptivity between the two germplasm materials. The Kentucky bluegrass consisted of three anthers, and each contained four pollen sacs that were divided into left and right halves. After meiosis, the microspore mother cells formed dyads and tetrads, which were primarily symmetrical and underwent mitosis to form three-celled pollen. Kentucky bluegrass has a one-locular ovary, two-feathery stigmas, thick nucleolar and anatropous ovules, and a typical polygonum embryo sac as its reproductive organs. The main type of apomixis observed was apospory, resulting in the coexistence of multiple embryo sacs. Polyembryonic seeds were frequently observed in Kentucky bluegrass due to apospory. Most importantly, our research found that apospory caused early embryogenesis during fertilization, which is a vital embryological feature for identifying sexual reproduction and apomixis in Kentucky bluegrass. Sexual reproduction followed strict double fertilization, while in apomixis a complete seed was only formed through pseudogamy. These embryological characteristics are documented here, and their study can aid in understanding the evolution of Kentucky bluegrass.

Genome Sequence Resource of Curvularia clavata Causing Leaf Spot Disease on Tobacco by Oxford Nanopore PromethION.

Genome Sequence Resource of Curvularia clavata Causing Leaf Spot Disease on Tobacco by Oxford Nanopore PromethION.

Genetic analysis and QTL mapping of domestication-related traits in chili pepper (Capsicum annuum L.).

Chili pepper (Capsicum annuum L.) is one of the oldest and most phenotypically diverse pre-Columbian crops of the Americas. Despite the abundance of genetic resources, the use of wild germplasm and landraces in chili pepper breeding is limited. A better understanding of the evolutionary history in chili peppers, particularly in the context of traits of agronomic interest, can contribute to future improvement and conservation of genetic resources. In this study, an F2:3 mapping population derived from a cross between a C. annuum wild accession (Chiltepin) and a cultivated variety (Puya) was used to identify genomic regions associated with 19 domestication and agronomic traits. A genetic map was constructed consisting of 1023 single nucleotide polymorphism (SNP) markers clustered into 12 linkage groups and spanning a total of 1,263.87cM. A reciprocal translocation that differentiates the domesticated genome from its wild ancestor and other related species was identified between chromosomes 1 and 8. Quantitative trait locus (QTL) analysis detected 20 marker-trait associations for 13 phenotypes, from which 14 corresponded to previously identified loci, and six were novel genomic regions related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. Our results revealed that the genetic architecture of Capsicum domestication is similar to other domesticated species with few loci with large effects, the presence of QTLs clusters in different genomic regions, and the predominance of domesticated recessive alleles. Our analysis indicates the domestication process in chili pepper has also had an effect on traits not directly related to the domestication syndrome. The information obtained in this study provides a more complete understanding of the genetic basis of Capsicum domestication that can potentially guide strategies for the exploitation of wild alleles.

Natural variation in HvAT10 underlies grain cell wall-esterified phenolic acid content in cultivated barley.

The phenolic acids, ferulic acid and p-coumaric acid, are components of plant cell walls in grasses, including many of our major food crops. They have important health-promoting properties in grain, and influence the digestibility of biomass for industrial processing and livestock feed. Both phenolic acids are assumed to be critical to cell wall integrity and ferulic acid, at least, is important for cross-linking cell wall components, but the role of p-coumaric acid is unclear. Here we identify alleles of a BAHD p-coumaroyl arabinoxylan transferase, HvAT10, as responsible for the natural variation in cell wall-esterified phenolic acids in whole grain within a cultivated two-row spring barley panel. We show that HvAT10 is rendered non-functional by a premature stop codon mutation in half of the genotypes in our mapping panel. This results in a dramatic reduction in grain cell wall-esterifed p-coumaric acid, a moderate rise in ferulic acid, and a clear increase in the ferulic acid to p-coumaric acid ratio. The mutation is virtually absent in wild and landrace germplasm suggesting an important function for grain arabinoxylan p-coumaroylation pre-domestication that is dispensable in modern agriculture. Intriguingly, we detected detrimental impacts of the mutated locus on grain quality traits where it was associated with smaller grain and poorer malting properties. HvAT10 could be a focus for improving grain quality for malting or phenolic acid content in wholegrain foods.

Genetic Diversity and Population Structure Analysis of Chinese Mitten Crab (Eriocheir sinensis) in the Yangtze and Liaohe Rivers

Recently, the economic traits of Chinese mitten crab (Eriocheir sinensis) varieties have had a negative tendency. Meanwhile, the status of wild germplasm resources of E. sinensis is unknown, hindering the utilization of wild germplasm resources and the green development of the E. sinensis industry. Thus, the conservation of the wild E. sinensis germplasm resource is of great significance. To this end, we collected wild E. sinensis from two different river basins, the Yangtze River basin, and the Liaohe River basin, and analyzed the genetic diversity as well as the genetic differentiation in E. sinensis populations. Based on eight microsatellite markers, we found moderate genetic diversity in E. sinensis populations regardless of river basin. Based on the mitochondrial D-loop region, we found that all populations are at mutation drift equilibrium, while the Nm between any two populations is greater than 1. We hypothesized the existence of island model gene flow patterns among E. sinensis. Interestingly, genetic differentiation among E. sinensis populations was low, except that between Liaohe and Anqing or Shanghai populations. Additionally, geometric morphological analysis could distinguish E. sinensis from different basins, with an accuracy of 94.2–100%. Given the similar genetic diversity in the two basins, the genetic convergence of E. sinensis from different basins deserves further attention.

The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia

BackgroudPaeonia holds considerable value in medicinal, ornamental horticultural, and edible oil industries, but the incomplete state of phylogenetic research in this genus poses a challenge to the effective conservation and development of wild germplasm, and also impedes the practical utilization of existing cultivars. Due to its uniparental inheritance and lack of recombination, the plastome (i.e., plastid genome), which is a valuable molecular marker for phylogenetic analyses, is characterized by an appropriate rate of nucleotide evolution.MethodsIn this study, 10 newly assembled data and available reported data were combined to perform a comparative genomics and phylogenetics analysis of 63 plastomes of 16 Paeonia species, primarily from East Asia, which is the origin and diversity center of Paeonia.ResultsRanging between 152,153 and 154,405 bp, most plastomes displayed a conserved structure and relatively low nucleotide diversity, except for six plastomes, which showed obvious IR construction or expansion. A total of 111 genes were annotated in the Paeonia plastomes. Four genes (rpl22, rps3, rps19 and ycf1) showed different copy numbers among accessions while five genes (rpl36, petN, psbI, rpl33 and psbJ) showed strong codon usage biases (ENC < 35). Additional selection analysis revealed that no genes were under positive selection during the domestication of tree peony cultivars whereas four core photosynthesis-related genes (petA, psaA, psaB and rbcL) were under positive selection in herbaceous peony cultivars. This discovery might contribute to the wide adaption of these cultivars. Two types of molecular markers (SSR and SNP) were generated from the 63 plastomes. Even though SSR was more diverse than SNP, it had a weaker ability to delimit Paeonia species than SNP. The reconstruction of a phylogenetic backbone of Paeonia in East Asia revealed significant genetic divergence within the P. ostii groups. Evidence also indicated that the majority of P. suffruticosa cultivars had a maternal origin, from P. ostii. The results of this research also suggest that P. delavayi var. lutea, which likely resulted from hybridization with P. ludlowii, should be classified as a lineage within the broader P. delavayi group.ConclusionsOverall, this study’s research findings suggest that the Paeonia plastome is highly informative for phylogenetic and comparative genomic analyses, and could be useful in future research related to taxonomy, evolution, and domestication.

Resequencing of Rosa rugosa accessions revealed the history of population dynamics, breed origin, and domestication pathways

BackgroundRosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions.ResultsA total of 19,041,284 SNPs were identified in 188 R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth.ConclusionsThe Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.