Identification of Cotton F1 Hybrids and their Parents through Molecular Marker under Salinity Stress

An experiment was carried out at Main Cotton Research Station, NAU, Surat, Gujarat, India during 2018–2020 to identify F1 hybrids and their parents through SSR marker for salinity tolerance in cotton. The four cotton parents (two salt tolerant and two salt sensitive) were crossed in a diallel fashion to obtain twelve cotton hybrids and subjected to DNA isolation and PCR amplification with SSR markers. In the present study, six SSR markers (TMB0409, DPL0094, BNL686, JESPR153, CM45 and MGHES006) were identified to be polymorphic between parents and the hybrids. The SSR primer TMB0409, DPL0094, JESPR153 and CM45 identified two fragments each from different parents in two, two, four and eight cotton hybrids, respectively, which confirmed true hybrids. Hence, the SSR molecular marker, individually or in combination can be used to distinguish and confirm the hybrid and parents in cotton with special reference to salinity. The PCA analysis revealed that BNL686–1 (248 bp) allele contributed significantly to the quantum of variation as explained by PC1. Hence, this allele is able to serve as a benchmark for ascertaining the efficient pattern of grouping between genotypes. Further, the marker CM45 amplified a fragment specific to the saline tolerant parents which was absent in sensitive parents as well as a fragment produced in sensitive parent which was absent in the tolerant parents, hence the molecular marker CM45 may associate with the salinity tolerance in cotton and can be used for salinity tolerant breeding program after confirming in a large population.

Exploring the Role of WRKY Transcription Factor in the Growth and Development of Bletilla striata based on Bioinformatics Analysis

WRKY type transcription factors (TFs) play crucial roles in the growth and development of plants. However, a comprehensive analysis of the WRKY family members in a valuable Chinese herbal orchid, Bletilla striata, or in other orchids, is limited. In this study, WRKY gene family was screened out from the transcriptome data of Bletilla striata by bioinformatics method. The 29 WRKY TFs that were identified from the B. striata genome and named BsWRKY1 to BsWRKY29 were divided into three clades: group Ⅰ (involving 8 WRKY sequences), group Ⅱ (18) and group Ⅲ (3), in which group Ⅱ was further divided into 5 subgroups: Ⅱ-a (involving 1 WRKY sequences), Ⅱ-b (5), and Ⅱ-c (3), Ⅱ-d (7), Ⅱ-e (3). EST-SSR marker mining test showed that 10 markers could be stably amplified with obvious polymorphisms among 4 landraces. Our data suggest that BsWRKY genes may work together to regulate plant growth and development. In different subcellular locations, BsWRKY genes not only played its own functions, but also coordinated the regulation of the whole life activities. Taken together, these results provided a theoretical basis for further studies on the gene functions and regulatory mechanisms of what in B. striata.

Analysis of Genetic Diversity of Myrtle (Myrtus Communis L.) by Using SSR Technique

This research carried out to compare some of the individuals of Myrtle from bushes in different environmental sites (Lattakia, Safita, Qusul Maaf, northern Aleppo and at different altitudes from the sea surface). The genetic diversity of 19 genotypes was tested using simple sequence repeats (SSRs) technique with 10 primers. The results of DNA extraction showed a high molecular size fragment as a band at the top of each lane, additionally to a partial degradation. At the end DNA concentration, integrity and purity were enough for SSR marker. Genetic variations were detected by SSR marker with similarity coefficient ranged between 0.08 – 0.89 based on Dice coefficient. Total of 27 alleles were scored from 19 genotypes, and the number of alleles was ranged between 2 (myrcom8 and 9) and 4 (myrcom2 and 6). The calculated value of polymorphism information content (PIC) was ≤ 0.5. Nineteen genotypes were distributed on three main clusters, two of them II and III included minimum number of genotypes from humid climate sites, while the majority of genotypes was distributed on cluster I in mixed manner.

Virulence and SSR Diversity of Brown Planthopper (Nilaparvata lugens) Adapted on Differential Rice Host Varieties

Brown planthopper biotype 1, 2, 3 and a representative field population are required for resistance screening of promising rice lines in Indonesia, but the current biotype stocks has shown deviation in virulence patterns. The objectives of this study were to develop a set of brown planthopper populations with differential virulence and to investigate their genetic variability using SSR marker. Females originated from two field populations were selected on variety Mudgo (carries Bph1 gene) or ASD7 (bph2 gene) using honeydew excretion as the virulence parameter. Selection cycles resulted in population T, M, A, and R, which was raised and adapted on variety TN1 (carries no Bph gene), Mudgo, ASD7, and Rathu Heenathi (Bph3, Bph17), respectively. Population R was the most virulent as expected and can be used to represent a field population, but the remaining populations still showed high virulence level. AMOVA and PCoA results based on analysis with 38 SSR primer pairs revealed partial genetic separation among populations, with population R was the most genetically distant from the remaining populations. The desired virulence character of the remaining populations is expected could be achieved after further selection and prolonged adaptation on their respective hosts.

SSR Marker-Based Genetic Resource Assessment of The Rainbow Clam Moerella Iridescens Along The Coasts of China: Implications for Strategy of Conservation Management

This study aims to determine the genetic structure and diversity of rainbow clam Moerella iridescens in different sea areas of China. Seventeen pairs of microsatellite primers (SSR) were used to amplify the SSRs of rainbow clam in Lianyungang of Haizhou Bay, Chongming of Shanghai, Ningde in Fujian, Cixi and Wenzhou in Zhejiang. A total of 1146 alleles were detected in 310 individuals from the 17 SSR loci. The average observed heterozygosity of six populations was 0.4381–0.6139, the average expected heterozygosity was 0.5897–0.7325, and the average Shannon diversity index was 1.2655–1.7998. The clams exhibited rich genetic diversity and the FST of the genetic differentiation index of the six populations was 0.0470, indicating low genetic differentiation amongst the populations. The results indictated that rainbow clam along China coasts exhibited high diversity and low population differentiation.

Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles

The genus Chaenomeles has long been considered an important ornamental, herbal and cash crop and is widely cultivated in East Asia. Traditional studies of Chaenomeles mainly focus on evolutionary relationships at the phenotypic level. In this study, we conducted RNA-seq on 10 Chaenomeles germplasms supplemented with one outgroup species, Docynia delavayi (D. delavayi), on the Illumina HiSeq2500 platform. After de novo assemblies, we generated from 40,084 to 49,571 unigenes for each germplasm. After pairwise comparison of the orthologous sequences, 9,659 orthologues within the 11 germplasms were obtained, with 6,154 orthologous genes identified as single-copy genes. The phylogenetic tree was visualized to reveal evolutionary relationships for these 11 germplasms. GO and KEGG analyses were performed for these common single-copy genes to compare their functional similarities and differences. Selective pressure analysis based on 6,154 common single-copy genes revealed that 45 genes were under positive selection. Most of these genes are involved in building the plant disease defence system. A total of 292 genes containing simple sequence repeats (SSRs) were used to develop SSR markers and compare their functions in secondary metabolism pathways. Finally, 10 primers were chosen as SSR marker candidates for Chaenomeles germplasms by comprehensive standards. Our research provides a new methodology and reference for future related research in Chaenomeles and is also useful for improvement, breeding and selection projects in other related species.