Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)

Novel centromeric repetitive DNA elements reveal karyotype dynamics in polyploid sainfoin (Onobrychis viciifolia)

Polyploidy is a common feature in eukaryotes with one of paramount consequences leading to better environmental adaptation. Heterochromatin is often located at telomeres and centromeres and contains repetitive DNA sequences. Sainfoin (Onobrychis viciifolia) is an important perennial forage legume for sustainable agriculture. However, there are only a few studies on the sainfoin genome and chromosomes. In this study, novel tandem repetitive DNA sequences of the sainfoin genome (OnVi180, OnVi169, OnVi176 and OnVidimer) were characterized using bioinformatics, molecular and cytogenetic approaches. The OnVi180 and OnVi169 elements colocalized within functional centromeres. The OnVi176 and OnVidimer elements were localized in centromeric, subtelomeric and interstitial regions. We constructed a sainfoin karyotype that distinguishes the seven basic chromosome groups. Our study provides the first detailed description of heterochromatin and chromosome structure of sainfoin and proposes an origin of heterozygous ancestral genomes, possibly from the same ancestral diploid species, not necessarily from different species, or for chromosome rearrangements after polyploidy. Overall, we discuss our novel and complementary findings in a polyploid crop with unique and complex chromosomal features.

A chromosome-level genome assembly for Onobrychis viciifolia reveals gene copy number gain underlying enhanced proanthocyanidin biosynthesis

Sainfoin (Onobrychis viciifolia), which belongs to subfamily Papilionoideae of Leguminosae, is a vital perennial forage known as "holy hay" due to its high contents of crude proteins and proanthocyanidins (PAs, also called condensed tannins) that have various pharmacological properties in animal feed, such as alleviating rumen tympanic disease in ruminants. In this study, we select an autotetraploid common sainfoin (2n = 4x = 28) and report its high-quality chromosome-level genome assembly with 28 pseudochromosomes and four haplotypes (~1950.14 Mb, contig N50 = 10.91 Mb). The copy numbers of genes involved in PA biosynthesis in sainfoin are significantly greater than those in four selected Fabales species, namely, autotetraploid Medicago sativa and three other diploid species, Lotus japonicus, Medicago truncatula, and Glycine max. Furthermore, gene expansion is confirmed to be the key contributor to the increased expression of these genes and subsequent PA enhancement in sainfoin. Transcriptomic analyses reveal that the expression of genes involved in the PA biosynthesis pathway is significantly increased in the lines with high PA content compared to the lines with medium and low PA content. The sainfoin genome assembly will improve our understanding of leguminous genome evolution and biosynthesis of secondary metabolites in sainfoin.

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

BACKGROUND

Amomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from different A. tsaoko tissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers.

RESULTS

A total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism in A. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72 A. tsaoko accessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the six A. tsaoko populations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species.

CONCLUSIONS

Our study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.

Analysis of genetic diversity among Onobrychis accessions with high agronomic performance by simple sequence repeat (SSR) markers

BACKGROUND

Onobrychis viciifolia Scop. is a short-lived perennial cool-season legume used for forage production. It is a common native species in Asia Minor, especially in Turkey, the districts of the Caucasus, and the Caspian fringes. It can grow well in a broad range of climatic and soil types found in Asia, Europe, and North America. It is a non-bloating crop, making it suitable for use in both hay and pasture.

METHODS AND RESULTS

The aim was to assess the diversity of the 83 sainfoin genotypes selected based on their high agronomic performance from a germplasm collection evaluated in the experimental field of Tekirdag Namik Kemal University, Turkey. Ten nuclear simple sequence repeat (nSSR) primers (OVK036, OVK046, OVK094, OVK101, OVK125, OVK161, OVK174, OVM033, OVM061, and OVM125) were used in the study. All nSSR loci were found to be polymorphic and totally 92 alleles were detected. The mean observed number of alleles per locus was calculated as 9.2. Among the genetic diversity parameters, Shannon Index (I = 0.375), unbiased genetic diversity value (uh = 0.243), and mean polymorphic information content (PIC = 0.240) were calculated. The genetic distance value varied between 0.43 and 0.95. Based on the dendrogram built by the UPGMA clustering method using genetic distance values, it was observed that the studied sainfoin genotypes were divided into two main clusters, whereas the STRUCTURE analysis results had high support for three clusters.

CONCLUSIONS

The results obtained from this study provide important information on the genetic structures of the studied sainfoin genotypes and their genetic relationship. Therefore acquired genetic data will be useful in designing more efficient polycross nurseries, allowing open pollination of best performing and genetically diverse genotypes in the isolated conditions, which will increase genetic gain in sainfoin breeding programs.

Legume Breeding for the Agroecological Transition of Global Agri-Food Systems: A European Perspective

Wider and more profitable legume crop cultivation is an indispensable step for the agroecological transition of global agri-food systems but represents a challenge especially in Europe. Plant breeding is pivotal in this context. Research areas of key interest are represented by innovative phenotypic and genome-based selection procedures for crop yield, tolerance to abiotic and biotic stresses enhanced by the changing climate, intercropping, and emerging crop quality traits. We see outmost priority in the exploration of genomic selection (GS) opportunities and limitations, to ease genetic gains and to limit the costs of multi-trait selection. Reducing the profitability gap of legumes relative to major cereals will not be possible in Europe without public funding devoted to crop improvement research, pre-breeding, and, in various circumstances, public breeding. While most of these activities may profit of significant public-private partnerships, all of them can provide substantial benefits to seed companies. A favorable institutional context may comprise some changes to variety registration tests and procedures.

De novo transcriptome assembly and EST-SSR markers development for Zelkova schneideriana Hand.-Mazz. (Ulmaceae)

Zelkova schneideriana Hand.-Mazz. of the Ulmaceae family is a Tertiary relict and economically deciduous tree species endemic to Central and Southern China. In this study, we performed a transcriptome sequencing of Z. schneideriana using high-throughput sequencing approach to detect polymorphic expressed sequence tag-simple sequence repeats (EST-SSR) markers. A total of 3,235 microsatellite loci were detected from 53,517 unigenes. A set of 30 microsatellite markers were randomly selected to validate in 41 individuals from three populations, of which 10 were polymorphic. The number of alleles per locus ranged from 3 to 11. The observed heterozygosity and expected heterozygosity ranged from 0.366 to 0.829 and 0.439 to 0.848, respectively. These polymorphic SSR primers showed good transferability across different Zelkova species, and are valuable for future studies on genetic diversity, conservation, phylogeography, and species delimitation in Z. schneideriana, as well as other Zelkova species.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02968-5.

High allelic diversity of the centromere-specific histone H3 (CENH3) in the legume sainfoin (Onobrychis viciifolia)

The centromere is a structurally and functionally specialized region on each eukaryotic chromosome and is essential for accurate and complete segregation of chromosomes during cell division. Centromeric nucleosomes differ from canonical nucleosomes by replacement of the histone H3 with its centromere-specific variant CENH3. CENH3 is essential for active centromeres in most eukaryotes. Homologs of CENH3 are identified in many organisms. Sainfoin (Onobrychis viciifolia) is an agriculturally important perennial forage and is a legume of the Fabaceae family. There is very limited information on the structure of the sainfoin genome and no data are available on its centromere structure. Here, we aim to characterize the sainfoin CENH3 homolog (OvCENH3). Using a sequence homology-based strategy with gene-specific primers, we were able to clone transcripts from sainfoin total RNA. The amplified clones were sequenced and compared by bioinformatics tools. Four distinct alleles of OvCENH3 were detected. Our study provides the first structural features on sainfoin centromeres with a possible allotetraploid origin for sainfoin. We discuss and compare our findings with that for other important legume species.

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China. However, a lack of suitable molecular markers hinders the genomic and genetic studies on this species. Here, we characterized and developed the microsatellite markers from a newly sequenced P. chienii transcriptome. A total of 21,835 microsatellite loci were detected from 161,131 non-redundant unigene sequences, and the frequency of SSRs was 13.55%, with an average of one SSR loci per 9.18 kb. Mono-nucleotide, di-nucleotide, and tri-nucleotide were the dominant repeat types, accounting for 50.06, 13.49, and 29.39% of the total SSRs, respectively. In terms of distribution location, the coding regions (CDS) with few microsatellites and mainly consisted of tri-nucleotides. There were significant differences in the length of microsatellite among genic regions and motif types. Functional annotation showed that the unigenes containing microsatellites had a wide range of biological functions, most of which were related to basic metabolism, and a few might be involved in expression regulation of gene and response to environmental stress. In addition, 375 primer pairs were randomly selected and synthesized for the amplification and validation of microsatellite markers. Seventy-seven primer pairs were successfully amplified and 40 primer pairs were found to be polymorphic. Finally, 20 pairs of primers with high polymorphism were selected to assess the genetic diversity in four P. chienii populations. In addition, the newly developed microsatellite markers exhibited high transferability (70%) in Amentotaxus argotaenia. Our study could enable further genetic diversity analysis and functional gene mining on Taxaceae.