A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data

Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources

Jujube (Ziziphus jujuba Mill.) is a commercially important tree native to China, known for its high nutritional value and widespread distribution, as well as its diverse germplasm resources. Being resilient to harsh climatic conditions, the cultivation of jujube could provide a solution to food insecurity and income for people of arid and semi-arid regions in and outside of China. The evaluation of germplasm resources and genetic diversity in jujube necessitates the use of Simple Sequence Repeat (SSR) markers. SSR markers are highly polymorphic and can be used to evaluate the genetic diversity within and between cultivars of Chinese jujube, and are important for conservation biology, breeding programs, and the discovery of important traits for Chinese jujube improvement in China and abroad. However, traditional methods of SSR development are time-consuming and inadequate to meet the growing research demands. To address this issue, we developed a novel approach called Multiple-Genome-Based SSR identification (MGB-SSR), which utilizes the genomes of three jujube cultivars to rapidly screen for polymorphic SSRs in the jujube genome. Through the screening process, we identified 12 pairs of SSR primers, which were then used to successfully classify 249 jujube genotypes. Based on the genotyping results, a digital ID card was established, enabling the complete identification of all 249 jujube plants. The MGB-SSR approach proved efficient in rapidly detecting polymorphic SSRs within the jujube genome. Notably, this study represents the first successful differentiation of jujube germplasm resources using 12 SSR markers, with 4 markers successfully identifying triploid jujube genotypes. These findings offer valuable information for the classification of Chinese jujube germplasm, thereby providing significant assistance to jujube researchers and breeders in identifying unknown jujube germplasm.

De Novo Mining and Validating Novel Microsatellite Markers to Assess Genetic Diversity in Maruca vitrata (F.), a Legume Pod Borer

Maruca vitrata (Fabricius) is an invasive insect pest capable of causing enormous economic losses to a broad spectrum of leguminous crops. Microsatellites are valuable molecular markers for population genetic studies; however, an inadequate number of M. vitrata microsatellite loci are available to carry out population association studies. Thus, we utilized this insect's public domain databases for mining expressed sequence tags (EST)-derived microsatellite markers. In total, 234 microsatellite markers were identified from 10053 unigenes. We discovered that trinucleotide repeats were the most predominant microsatellite motifs (61.53%), followed by dinucleotide repeats (23.50%) and tetranucleotide repeats (14.95%). Based on the analysis, twenty-five markers were selected for validation in M. vitrata populations collected from various regions of India. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) ranged from 2 to 5; 0.00 to 0.80; and 0.10 to 0.69, respectively. The polymorphic loci showed polymorphism information content (PIC), ranging from 0.09 to 0.72. Based on the genetic distance matrix, the unrooted neighbor-joining dendrogram differentiated the selected populations into two discrete groups. The SSR markers developed and validated in this study will be helpful in population-level investigations of M. vitrata to understand the gene flow, demography, dispersal patterns, biotype differentiation, and host dynamics.

Analysis of Genetic Diversity of Banana Weevils (Cosmopolites sordidus) (Coleoptera: Curculionidae) Using Transcriptome-Derived Simple Sequence Repeat Markers

The banana weevil, Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) is an economically important insect pest of bananas. It causes up to 100% yield losses and substantial lifespan reduction in bananas. Advances in genomics, proteomics, and sequencing technologies have provided powerful pathways to genotyping disastrous pests such as C. sordidus. However, such technologies are often not available to the majority of rural subtropical African banana growers and pest control managers. This study was therefore motivated by the need to create cheap and easily accessible C. sordidus genotyping methods that could be deployed by banana pest control managers to the benefit of C. sordidus control programs in the tropics where such advanced technologies are not readily accessible. We used an in-house C. sordidus transcriptome from the an-ongoing study from which we mined an array of simple sequence repeat (SSR) markers. Of these, six highly polymorphic transcriptome-derived SSR markers were used to successfully genotype within and among banana weevil population genetic diversity of 12 C. sordidus populations collected from four banana-growing agro-ecological zones (AEZs) in Uganda. The developed transcriptome-derived SSR markers can be used by researchers in population genetics for characterization of the C. sordidus and identification of new genes that are linked to traits of particular interest. The significant genetic diversity revealed in C. sordidus provides pertinent information for integrated pest management strategies.