SSR MARKERS REVEALED GENETIC DIVERGENCE OF RICE BROWN PLANTHOPPER POPULATIONS MAINTAINED ON TWO SETS OF DIFFERENTIAL HOST VARIETIES

<p>Resistance screening of promising rice lines in Indonesia requires the use of brown planthopper (BPH) biotypes 1, 2, and 3. Three BPH populations have been raised as biotypes 1, 2, and 3 on differential rice host of improved varieties Pelita I-1 (no <em>Bph </em>gene), IR26 (<em>Bph1</em>), and IR42 (<em>bph2</em>), respectively. Three alternative populations have also been developed on the respective traditional varieties TN1 (no <em>Bph </em>gene), Mudgo (<em>Bph1</em>), and ASD7 (<em>bph2</em>). Although these populations displayed two virulent patterns other than biotype 1 to 3 phenotypes, they were expected to be discriminated into two virulence groups by SSR analysis. The study aimed to investigate the level of genetic variation among the six BPH populations using SSR markers and to relate it with the observed virulence patterns. Genotyping of 30 females with 29 polymorphic SSR markers revealed higher genetic parameter values in populations reared on improved varieties than those on traditional varieties. This difference was marked as two population clusters in PCoA plots corresponding to the host variety type, in contrast to the previous assumption that clustering would be based on virulence patterns. The presence of individuals with unwanted virulence allele, either resulting from contamination during the long period of rearing or lack of host adaptation period, is suspected. The result of this study indicates that the six populations are not suitable for resistance screening. Virulence selection must be performed until they attain biotype 1 to 3 phenotypes which can be genetically separated by DNA markers.</p>

Agro-morphological and molecular diversity in different maturity groups of Indian cauliflower (Brassica oleracea var. botrytis L.)

The present study analysed the molecular and agro-morphological diversity in a set of 92 diverse cauliflower genotypes and two each of cabbage and broccoli. Field evaluation of the genotypes was done in randomized block design (RBD) at two locations (i.e. IARI, New Delhi and ICAR-RC-NEH Region, Barapani) during Rabi2019-20. Genotypes showed variation for all the eight observed traits at both locations and, the differences in early and snowball groups were distinct. Pusa Meghna, DC-33-8, Pusa Kartiki and CC-14 were earliest for curd initiation. Genotypes showed higher values for curd traits at Delhi. Molecular diversity was detected with 90 polymorphic simple sequence repeats (SSR). Number of alleles ranged from 1 to 9 with mean value of 2.16 and the highest polymorphic information content (PIC) value was observed for primer BoGMS0742 (0.68) with a mean value of 0.18. Cluster analysis using agro-morphological traits substantiated classification of the genotypes for maturity groups. However, SSR analysis revealed four clusters and with a composite pattern of genotype distribution. STRUCTURE analysis also supported the admixture and four subpopulations. The studyindicates for introgression of genetic fragments across the maturity groups, thereby, potential for use in further genetic improvement and heterosis breeding.

Comparative Transcriptome Analysis of the Roots and Leaves of Bupleurum Chinense DC. Seedlings Under Drought Stress

Background drought stress is one of the important environmental factors affecting the quality and yield of medicinal materials, and is the main factor restricting the field production of Bupleurum chinense. B. chinense seedlings sensitive to low moisture, but there are few reports on the molecular mechanism of B. chinense seedlings under drought stress. Therefore, the transcriptome of the leaves and roots of B. chinense seedlings before and after drought were analyzed by Illumina sequencing technology and bioinformatics analysis. Results a total of 59.82 GB of clean data was obtained, and the unigenes were compared with Nr, Swissprot, String, GO, KEGG, and Pfam databases. Under drought stress, 3,737 and 6,816 differentially expressed genes (DEGs) were identified in leaves and roots of B. chinense, respectively. The obtained DEGs from leaves and roots were classified into 37, and 36 GO terms and were involved in 222 and 253 KEGG pathways, respectively. SSR analysis were obtained identified 33,728 loci, wherein dinucleotides accounted for the largest proportion. Genes involved in diterpenoid and unsaturated fatty acid biosynthesis were significantly over-expressed in roots under drought stress, suggesting these two cellular processes underpin the adaptation and resistance of B. chinense seedlings to drought stress. Conclusions the results provided a theoretical basis for further identification of the molecular mechanism of drought resistance and breeding of drought resistance varieties of B. chinense.

Full-Length SMRT Transcriptome Sequencing and SSR Analysis of Bactrocera dorsalis (Hendel)

Bactrocera dorsalis (Hendel), as one of the most notorious and destructive invasive agricultural pests in the world, causes damage to over 250 different types of fruits and vegetables throughout tropical and subtropical areas. PacBio single-molecule real-time (SMRT) sequencing was used to generate the full-length transcriptome data of B. dorsalis. A total of 40,319,890 subreads (76.6 Gb, clean reads) were generated, including 535,241 circular consensus sequences (CCSs) and 386,916 full-length non-concatemer reads (FLNCs). Transcript cluster analysis of the FLNC reads revealed 22,780 high-quality reads (HQs). In total, 12,274 transcripts were functionally annotated based on four different databases. A total of 1978 SSR loci were distributed throughout 1714 HQ transcripts, of which 1926 were complete SSRs and 52 were complex SSRs. Among the total SSR loci, 2–3 nucleotide repeats were dominant, occupying 83.62%, of which di- and tri- nucleotide repeats were 39.38% and 44.24%, respectively. We detected 105 repeat motifs, of which AT/AT (50.19%), AC/GT (39.15%), CAA/TTG (32.46%), and ACA/TGT (10.86%) were the most common in di- and tri-nucleotide repeats. The repeat SSR motifs were 12–190 bp in length, and 1638 (88.02%) were shorter than 20 bp. According to the randomly selected microsatellite sequence, 80 pairs of primers were designed, and 174 individuals were randomly amplified by PCR using primers. The number of primers that had amplification products with clear bands and showed good polymorphism came to 41, indicating that this was a feasible way to explore SSR markers from the transcriptomic data of B. dorsalis. These results lay a foundation for developing highly polymorphic microsatellites for researching the functional genomics, population genetic structure, and genetic diversity of B. dorsalis.

IMPROVED SSRs-BASED GENETIC DIVERSITY ASSESSMENT OF COCONUTS (COCOS NUCIFERA L) ALONG THE COAST OF KENYA

ABSTRACTCoconut is the most important cash crop along the Coast of Kenya, yet its genetic diversity has not been fully established. A genetic diversity study of 48 coconut genotypes that were collected along the Coast of Kenya was conducted with 13 polymorphic short sequence repeats (SSRs) markers. SSR analysis was performed using GeneMapper while data analysis was done with PowerMarker and DARwin softwares.The results revealed a total of 68 alleles ranging from 2 to 11 per locus with a mean of 5.23 per marker. Gene diversity and polymorphic information content (PIC) ranged between 0.41 to 0.83 and 0.33 to 0.79, respectively. A neighbour-joining dendrogram grouped the genotypes into three major clusters containing distinct sub-clusters. This study underscored that capillary electrophoresis is a more accurate and informative technique for SSRs allele scoring than agarose gels, which was reported in a previous study with the same SSRs markers and coconut genotypes in Kenya. The clusters observed forms the basis to isolate conservation blocks, which are the key to establishing a genebank, since there is no documented coconut genebank for ex-situ conservation in Kenya.

The efficiency of SSR and ISSR markers for the assessment of genetic polymorphism of varieties and hybrids of garden chrysanthemum (Chrysanthemum × hortorum Bailey)

The genetic analysis of five varieties and seventeen hybrids of the collection of the Federal Research Centrethe Subtropical Scientific Centre of the Russian Academy of Sciences (FRC SSC RAS) of Sochi was carried out using DNAmarkers: SSR analysis and ISSR analysis. With the help of these markers, it was possible to identify the genetic differencesof the studied samples. At the same time, the analysis of phenotypic traits was carried out, which allowed us to dividethe studied plants into phenotypic groups. When processing genotypic and phenotypic groups, five related groups ofthe studied plants were identified. SSR-and ISSR-markers allow us to evaluate the genetic polymorphism of varieties andhybrids of Chrysanthemum × hortorum.

Investigation of the Genetic Structure of Some Common Bean (Phaseolus vulgaris L.) Commercial Varieties and Genotypes Used as a Genitor with SSR and SNP markers

Common bean is a species belonging to the Phaseolus genus of the Leguminosae family. It has economic importance due to being rich in protein, vitamin A and C, and minerals. Being one of the most cultivated species of legumes, the determination of genetic diversity in bean genotypes or populations has an important role in terms of our genetic resources. The objective of this study was to evaluate the genetic structure of 94 genotypes which were cultivated in different parts of the world and our country with SSR and SNP markers. 10 SSR loci and 73 SNP primers were used for the determination of genetic structure in commercial cultivars and breeding lines. All of the SSR and SNP loci used in the study were found to be polymorphic. A total of 89 alleles were identified for 10 SSR loci. Mean number of alleles per locus (Na=8.9), effective allele number (Ne=3.731), Shannon information index (I=1.468), observed heterozygosity (Ho=0.023), and expected heterozygosity (He=0.654) were calculated based on SSR analysis. According to the results of Bayesian-based STRUCTURE analysis using SSR and SNP data, 94 bean genotypes were genetically divided into three main clusters. According to genetic similarity based UPGMA dendrogram obtained from SSR and SNP analysis, 94 bean genotypes were divided into 2 main clusters. The obtained results provide important information about the genetic structures of the studied bean cultivars and breeding lines. With the obtained results, it will be possible to develop breeding programs to develop new cultivars by using our gene resources.

SSR analysis of modern Russian potato varieties using DNA samples of nomenclatural standards

The N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) is developing new approaches to documentation of national cultivars, taking into account recommendations of the International Code of Nomenclature for Cultivated Plants in parallel with methods of genetic certification. The nomenclatural standard of a particular cultivar represented by a herbarium specimen can be used as a reference for verifying authenticity and uniformity of cultivar specimens obtained from various sources. The verification requires fast and reliable methods for cultivar genotyping. This paper presents protocols for modified methods of DNA extraction, PCR-analysis and SSR-genotyping, which allow potato cultivars identification without the use of expensive reagent kits. A set of ten chromosome-specific microsatellite markers was used to study polymorphisms in 66 modern Russian potato cultivars, as well as in 11 pre-cultivars and breeding clones, represented by nomenclatural standards and voucher specimens, respectively. This subset of 77 specimens has demonstrated a high level of polymorphism in ten studied microsatellite loci. The SSR analysis identified 73 alleles; 7.3 alleles per locus were observed on average, the number of which varied from 3 (STG0025 locus) to 11 (locus StI046). The PIC values varied from 0.544 (STG0025 locus) to 0.836 (StI046 locus). The alleles, unique for this subset, were found at six studied loci. The high level of polymorphism at the SSR loci made it possible to unambiguously identify almost every cultivar, with the exception of the expected coincidence of microsatellite profiles of two cultivars, which are somaclonal variants. Using an optimized set of eight microsatellite markers, the genetic relationships of modern Russian potato cultivars were studied.

Agro-Morphological and Molecular Variability among Algerian Faba Bean (Vicia faba L.) Accessions

Faba bean (Vicia faba L.) Algerian accessions represent an essential source of traits of interest for crop improvement, especially for tackling climate change, because their genetic background and potential have not been well studied. The purpose of this research was to assess the genetic variability of 14 Algerian faba bean accessions by means of 10 agro-morphological traits and 7 simple sequence repeat markers (SSRs). ANOVA analysis showed a large significant phenotypic variation in fruit setting (FS), seed length (SL), seed width (SW), and 100-seeds weight (HSW), which arose as the main discriminant characters as revealed by principal component analysis (PCA). In addition, SSR analysis identified a total of twenty different alleles within our collection with a mean of 2.85 alleles per locus. The polymorphism information content (PIC) ranged from 0.32 to 0.58, with a mean of 0.44. Observed heterozygosity (Ho) ranged from 0.57 to 1.00 with a mean of 0.72, while the expected one (He) varied from 0.42 to 0.67, reaching a mean of 0.57. Based on agro-morphological as well as molecular data, the 14 accessions were not clustered according to the geographical pattern, as also confirmed by principal coordinate analysis (PCoA). Moreover, AMOVA highlighted that most of the overall genetic variation within our collection was the result of strong differentiation among accessions (84%). Finally, the Mantel test revealed that there was no substantial correlation between the molecular and agro-morphological traits (r = −0.025, p > 0.05). These findings represent a first step toward faba been breeding programs establishment in Algeria, indicating that our collection exhibited optimal agro- and molecular diversity to identify specific traits useful in Mediterranean environment.