Frequent germplasm exchanges drive the high genetic diversity of Chinese-cultivated common apricot germplasm

New insights into the evolution and local adaptation of the genus Castanea in east Asia

Chestnut plants (Castanea) are important nut fruit trees worldwide. However, little is known regarding the genetic relationship and evolutionary history of different species within the genus. How modern chestnut plants have developed local adaptation to various climates remains a mystery. The genomic data showed that Castanea henryi first diverged in the Oligocene ~31.56 million years ago, followed by Castanea mollissima, and the divergence between Castanea seguinii and Castanea crenata occurred in the mid-Miocene. Over the last 5 million years, the population of chestnut plants has continued to decline. A combination of selective sweep and environmental association studies was applied to investigate the genomic basis of chestnut adaptation to different climates. Twenty-two candidate genes were associated with temperature and precipitation. We also revealed the molecular mechanism by which CmTOE1 interacts with CmZFP8 and CmGIS3 to promote the formation of non-glandular trichomes for adaptation to low temperature and high altitudes. We found a significant expansion of CER1 genes in Chinese chestnut (C. mollissima) and verified the CmERF48 regulation of CmCER1.6 adaptation to drought environments. These results shed light on the East Asian chestnut plants as a monophyletic group that had completed interspecific differentiation in the Miocene, and provided candidate genes for future studies on adaptation to climate change in nut trees.

A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline

BACKGROUND

Although sequencing technologies have boosted the measurement of the genomic diversity of plant crops, it remains challenging to accurately genotype millions of genetic variants, especially structural variations, with only short reads. In recent years, many graph-based variation genotyping methods have been developed to address this issue and tested for human genomes. However, their performance in plant genomes remains largely elusive. Furthermore, pipelines integrating the advantages of current genotyping methods might be required, considering the different complexity of plant genomes.

RESULTS

Here we comprehensively evaluate eight such genotypers in different scenarios in terms of variant type and size, sequencing parameters, genomic context, and complexity, as well as graph size, using both simulated and real data sets from representative plant genomes. Our evaluation reveals that there are still great challenges to applying existing methods to plants, such as excessive repeats and variants or high resource consumption. Therefore, we propose a pipeline called Ensemble Variant Genotyper (EVG) that can achieve better genotyping performance in almost all experimental scenarios and comparably higher genotyping recall and precision even using 5× reads. Furthermore, we demonstrate that EVG is more robust with an increasing number of graphed genomes, especially for insertions and deletions.

CONCLUSIONS

Our study will provide new insights into the development and application of graph-based genotyping algorithms. We conclude that EVG provides an accurate, unbiased, and cost-effective way for genotyping both small and large variations and will be potentially used in population-scale genotyping for large, repetitive, and heterozygous plant genomes.

Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot

Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.

Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis

Apricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.

Comparative analysis of KNOX genes and their expression patterns under various treatments in Dendrobium huoshanense

Introduction

KNOX plays a pivotal role in governing plant growth, development, and responses to diverse abiotic and biotic stresses. However, information on the relationship between the KNOX gene family and expression levels under different treatments in Dendrobium is still limited.

Methods

To address this problem, we first used bioinformatics methods and revealed the presence of 19 KNOX genes distributed among 13 chromosomes in the Dendrobium huoshanense genome. Through an analysis of phylogenetic relationships, these genes were classified into three distinct clades: class I, class II, and class M. Our investigation included promoter analysis, revealing various cis-acting elements associated with hormones, growth and development, and abiotic stress responses. Additionally, qRT-PCR experiments were conducted to assess the expression patterns of DhKNOX genes under different treatments, including ABA, MeJA, SA, and drought.

Results

The results demonstrated differential expression of DhKNOX genes in response to these treatments, thereby highlighting their potential roles in stress adaptation.

Discussion

Overall, our results contribute important insights for further investigations into the functional characterization of the Dendrobium KNOX gene family, shedding light on their roles in plant development and stress responses.

The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties

The domestication process in long-lived plant perennials differs dramatically from that of annuals, with a huge amount of genetic exchange between crop and wild populations. Though apple is a major fruit crop grown worldwide, the contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense study. We used population genomics approaches to investigate the contributions of several wild apple species to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow. Population genetic structure inferences revealed that the East Asian wild apples, Malus baccata (L.) Borkh and M. hupehensis (Pamp.), form a single panmictic group, and that the European dessert and rootstock apples form a specific gene pool whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools, suggesting different evolutionary histories of European and Chinese apple varieties. Coalescent-based inferences and gene flow estimates indicated that M. baccata - M. hupehensis contributed to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions, and not as an initial contributor as previously supposed. We also confirmed the contribution through wild-to-crop introgressions of Malus sylvestris Mill. to the cultivated apple genome. Apple tree domestication is therefore one example in woody perennials that involved gene flow from several wild species from multiple geographical areas. This study provides an example of a complex protracted process of domestication in long-lived plant perennials, and is a starting point for apple breeding programmes.

Genetic and molecular dissection of ginseng (Panax ginseng Mey.) germplasm using high-density genic SNP markers, secondary metabolites, and gene expressions

Genetic and molecular knowledge of a species is crucial to its gene discovery and enhanced breeding. Here, we report the genetic and molecular dissection of ginseng, an important herb for healthy food and medicine. A mini-core collection consisting of 344 cultivars and landraces was developed for ginseng that represents the genetic variation of ginseng existing in its origin and diversity center. We sequenced the transcriptomes of all 344 cultivars and landraces; identified over 1.5 million genic SNPs, thereby revealing the genic diversity of ginseng; and analyzed them with 26,600 high-quality genic SNPs or a selection of them. Ginseng had a wide molecular diversity and was clustered into three subpopulations. Analysis of 16 ginsenosides, the major bioactive components for healthy food and medicine, showed that ginseng had a wide variation in the contents of all 16 ginsenosides and an extensive correlation of their contents, suggesting that they are synthesized through a single or multiple correlated pathways. Furthermore, we pair-wisely examined the relationships between the cultivars and landraces, revealing their relationships in gene expression, gene variation, and ginsenoside biosynthesis. These results provide new knowledge and new genetic and genic resources for advanced research and breeding of ginseng and related species.

A Chromosome-Level Genome of 'Xiaobaixing' (Prunus armeniaca L.) Provides Clues to Its Domestication and Identification of Key bHLH Genes in Amygdalin Biosynthesis

Apricot is a widely cultivated fruit tree of the drupe family, and its sweet/bitter kernel traits are important indicators of the quality and merchantability of apricots. The sweetness/bitterness traits were mainly determined by amygdalin content. However, the lack of high-quality genomes has limited insight into the traits. In this study, a high-quality genome of 'Xiaobaixing' was obtained by using single-molecule sequencing and chromosome-conformation capture techniques, with eight chromosomes of 0.21 Gb in length and 52.80% repetitive sequences. A total of 29,157 protein-coding genes were predicted with contigs N50 = 3.56 Mb and scaffold N50 = 26.73 Mb. Construction of phylogenetic trees of 15 species of Rosaceae fruit trees, with 'Xiaobaixing' differentiated by 5.3 Ma as the closest relative to 'Yinxiangbai'. GO functional annotation and KEGG enrichment analysis identified 227 specific gene families to 'Xiaobaixing', with 569 expansion-gene families and 1316 contraction-gene families, including the significant expansion of phenylalanine N-monooxygenase and β-glucosidase genes associated with amygdalin synthesis, significant contraction of wild black cherry glucoside β-glucosidase genes, amygdalin β-glucosidase genes, and β-glucosidase genes, and significant enrichment of positively selected genes in the cyanogenic amino acid metabolic pathway. The 88 bHLH genes were identified in the genome of 'Xiaobaixing', and ParbHLH66 (rna-Par24659.1) was found to be a key gene for the identification of sweet/bitter kernels of apricots. The amino acid sequence encoded by its gene is highly conserved in the species of Prunus mume, Prunus dulcis, Prunus persica, and Prunus avium and may be participating in the regulation of amygdalin biosynthesis, which provides a theoretical foundation for the molecular identification of sweet/bitter kernels of apricots.

Effects of Reactive Oxygen Levels on Chilling Injury and Storability in 21 Apricot Varieties from Different Production Areas in China

The key factors for resistance to chilling injury in apricot fruits were obtained by analyzing the low-temperature storage characteristics of 21 varieties of apricot fruits in the main producing areas of China. Twenty-one varieties of apricots from different production areas in China were stored at 0 °C for 50 d and then shelved at 25 °C. The storage quality, chilling injury, reactive oxygen species (ROS), antioxidant ability, and contents of bioactive substances of the apricots were measured and analyzed. The results showed that the 21 varieties of apricot fruits could be divided into two categories according to tolerance during low-temperature storage, where there was chilling tolerance and lack of chilling tolerance. Eleven varieties of apricots, of which Xiangbai and Yunbai are representative, suffered from severe chilling injury after cold storage and shelf life. After 50 d of storage at 0 °C, the levels of superoxide anions and hydrogen peroxide accumulated in the 11 varieties of apricots with a lack of chilling tolerance during storage were significantly higher than those in the remaining 10 varieties of apricots with chilling tolerance. In addition, the activities of ROS scavenging enzymes, represented by superoxide dismutase, catalase and peroxidase, were significantly decreased in 11 varieties of apricots with a lack of chilling tolerance during storage. The contents of bioactive substances with ROS scavenging ability, represented by ascorbic acid, total phenols, carotenoids, and total flavonoids, also significantly decreased. The 10 varieties of apricots, of which Akeximixi and Suanmao are representative, were less affected by chilling injury because the production and removal of ROS were maintained at normal levels, avoiding the damaging effects of ROS accumulation in the fruit. In addition, the 10 apricot varieties with chilling tolerance during storage had higher sugar and acid contents after harvest. This could supply energy for physiological metabolism during cold storage and provide carbon skeletons for secondary metabolism, thus enhancing the chilling tolerance of the fruits. Based on the results of cluster analysis combined with the geographical distribution of the 21 fruit varieties, it was found that apricot varieties with chilling tolerance during storage were all from the northwestern region of China where diurnal temperature differences and rapid climate changes occur. In conclusion, maintaining the balance of ROS production and removal in apricots during cold storage is a key factor to enhance the storage tolerance of apricots. Moreover, apricots with higher initial glycolic acid and bioactive substance contents are less susceptible to chilling injury.

Re-sequencing and morphological data revealed the genetics of stone shell and kernel traits in apricot

Kernel-using apricot (Prunus armeniaca L.) is an economically important fruit tree species in arid areas owing to its hardiness and cold and drought tolerance. However, little is known about its genetic background and trait inheritances. In the present study, we first evaluated the population structure of 339 apricot accessions and the genetic diversity of kernel-using apricots using whole genome re-sequencing. Second, the phenotypic data of 222 accessions were investigated for two consecutive seasons (2019 and 2020) for 19 traits, including kernel and stone shell traits and the pistil abortion rate of flowers. Heritability and correlation coefficient of traits were also estimated. The stone shell length (94.46%) showed the highest heritability, followed by the length/width ratio (92.01%) and length/thickness ratio (92.00%) of the stone shell, whereas breaking force of the nut (17.08%) exhibited a very low heritability. A genome-wide association study (GWAS) using general linear model and generalized linear mixed model revealed 122 quantitative trait loci (QTLs). The QTLs of the kernel and stone shell traits were unevenly assigned on the eight chromosomes. Out of the 1,614 candidate genes identified in the 13 consistently reliable QTLs found using the two GWAS methods and/or in the two seasons, 1,021 were annotated. The sweet kernel trait was assigned to chromosome 5 of the genome, similar to the almond, and a new locus was also mapped at 17.34-17.51 Mb on chromosome 3, including 20 candidate genes. The loci and genes identified here will be of significant use in molecular breeding efforts, and the candidate genes could play essential roles in exploring the mechanisms of genetic regulation.

Comparative Anatomical and Transcriptomics Reveal the Larger Cell Size as a Major Contributor to Larger Fruit Size in Apricot

Fruit size is one of the essential quality traits and influences the economic value of apricots. To explore the underlying mechanisms of the formation of differences in fruit size in apricots, we performed a comparative analysis of anatomical and transcriptomics dynamics during fruit growth and development in two apricot cultivars with contrasting fruit sizes (large-fruit Prunus armeniaca 'Sungold' and small-fruit P. sibirica 'F43'). Our analysis identified that the difference in fruit size was mainly caused by the difference in cell size between the two apricot cultivars. Compared with 'F43', the transcriptional programs exhibited significant differences in 'Sungold', mainly in the cell expansion period. After analysis, key differentially expressed genes (DEGs) most likely to influence cell size were screened out, including genes involved in auxin signal transduction and cell wall loosening mechanisms. Furthermore, weighted gene co-expression network analysis (WGCNA) revealed that PRE6/bHLH was identified as a hub gene, which interacted with 1 TIR1, 3 AUX/IAAs, 4 SAURs, 3 EXPs, and 1 CEL. Hence, a total of 13 key candidate genes were identified as positive regulators of fruit size in apricots. The results provide new insights into the molecular basis of fruit size control and lay a foundation for future breeding and cultivation of larger fruits in apricot.

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

BACKGROUND

Rosa 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.

RESULTS

A 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.

CONCLUSIONS

The 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.

Biodiversity Evaluation and Preservation of Italian Stone Fruit Germplasm (Peach and Apricot) in Southern Italy

The Prunus genus encompasses a group of economically important and closely related crops, sharing an essentially common genome and, thereby, a high level of conserved and transferable microsatellite (SSR) loci. In Southern Italy, many of the local and/or neglected varieties are abandoned and at risk of extinction due to the high degree of urbanization and agricultural intensification, despite their value as genetic resources for crop improvement. This research aimed to genetically and morphologically characterize the traditional apricot (P. armenica) and peach (P. persica) germplasms collected in old family orchards. Most of the official descriptor categories were scored, thus revealing a rather high level of phenotypic variation in both collections. Genetic data allowed the discovery of diversity masked by morphological traits. Genotyping in 15 and 18 SSRs, eight of which were transferable across both species, showed an average polymorphic informativeness (PIC) of 0.44 and 0.59 for apricot and peach, respectively, and a total of 70 and 144 alleles. A reliable identification of each genotype was achieved, and the presence of possible mislabeling and/or erroneous denominations was solved. These results are encouraging for the valorization of the still poorly explored Italian Prunus germplasm, with significant economic consequences for bioresource conservation and management.

Genome-wide identification of three-amino-acid-loop-extension gene family and their expression profile under hormone and abiotic stress treatments during stem development of Prunus mume

Transcription factors encoded by the three-amino-acid-loop-extension (TALE) gene family play a key role in regulating plant growth and development, and are involved in plant hormone regulatory pathways and responses to various environmental stresses. Researchers are currently studying TALE genes in different species, but Prunus mume TALE genes have not yet been studied. Therefore, based on the P. mume genome, we found a total of 23 TALE gene family members, which were distributed on eight chromosomes. TALE genes contained the characteristic domains of this family, and could be divided into KNOTTED-like homeobox (KNOX) subfamily and BEL1-like homeobox (BELL) subfamily. They can form heterodimers with each other. Fragment duplication and tandem duplication events were the main reasons for the expansion of P. mume TALE gene family members and the TALE genes were selected by different degrees of purification. The inter-species collinearity analysis showed that the relationship between P. mume and other four Prunus species was consistent with the distance of origin. Eleven members of P. mume TALE genes were specifically highly expressed in stem, mainly at the early stage of stem development. The cis-element analysis showed that the promoter of P. mume TALE genes contained a variety of hormone and abiotic stress response elements, and four TALE genes responded to two kinds of abiotic stresses and four kinds of hormones at the early stage of stem development. In conclusion, this study lays a foundation to explore the role of TALE gene family in P. mume growth and development.

Genetic diversity of Prunus armeniaca L. var. ansu Maxim. germplasm revealed by simple sequence repeat (SSR) markers

The genetic diversity and genetic structure of P. armeniaca var. ansu were analyzed based on SSR markers. The aim was to provide scientific basis for conservation, efficient utilization, molecular marker assisted breeding and improved variety selection of P. armeniaca var. ansu germplasm resources. The results showed that the level of genetic diversity within the population was high. Among the 30 SSR markers, the mean number of observed alleles was 11.433, the mean number of effective alleles was 4.433, the mean of Shannon information index was 1.670, and the mean of polymorphic information content was 0.670. Among the eight provenances, Tuanjie Township, Xinyuan County, Xinjiang had the highest genetic diversity. The observed alleles, effective alleles, Shannon information index and Nei’s gene diversity index among provenances were higher than those within provenances. Based on Bayesian mathematical modeling and UPGMA cluster analysis, 86 P. armeniaca var. ansu accessions were divided into three subpopulations and four groups, which reflected individual differences in provenances. Subpopulations classified by Bayesian mathematical modeling and groups classified by UPGMA cluster analysis were significantly correlated with geographical provenance (Sig<0.01) and the provenances significantly impacted classification of groups. The provenances played an important role in classification of groups. The genetic distance between Tuanjie Township of Xinyuan County and Alemale Township of Xinyuan County was the smallest, while the genetic relationship between them was the closest and the degree of genetic differentiation was small.