Role of microsatellites in genetic analysis of Bombyx mori silkworm: a review

Genome-Wide Microsatellites in Acanthopagrus latus: Development, Distribution, Characterization, and Polymorphism

The yellowfin seabream (Acanthopagrus latus) is an economically important commercial mariculture fish in China and Southeast Asia. Only a few simple sequence repeats (SSRs) of A. latus have been isolated and reported, which has hindered breeding progress. A total of 318,862 SSRs were isolated and characterized from the A. latus genome in this study. All SSRs were 9,069,670 bp in length, accounting for 1.32% of the genome. The density and frequency of SSRs were 468.40 loci/Mb and 13,323.19 bp/Mb, respectively. The major SSRs were dinucleotides (accounting for 76.92%), followed by trinucleotides (15.75%). The most abundant SSR motif was (AC)n (168,390, accounting for 53%), with the highest frequency (245.78 loci/Mb) and density (7304.18 bp/Mb). Most SSRs were located in non-coding regions, such as intergenic regions (34.54%) and introns (56.91%). SSR-containing exons were distributed into 51 gene ontology (GO) terms and significantly enriched in immunity- and growth-related pathways. A total of 217,791 SSR markers were successfully designed. Nine SSR markers were amplified in 29 A. latus individuals, and eight of them possess high polymorphism. The cross-species transferability of 33 out of the 37 tested loci were successfully amplified in Acanthopagrus schlegelii. These results lay the foundation for the molecular marker-assisted breeding and genetic information assessment of A. latus.

Dynamics of nuclear matrix attachment regions during 5th instar posterior silk gland development in Bombyx mori

Background

Chromatin architecture is critical for gene expression during development. Matrix attachment regions (MARs) control and regulate chromatin dynamics. The position of MARs in the genome determines the expression of genes in the organism. In this study, we set out to elucidate how MARs temporally regulate the expression of the fibroin heavy chain (FIBH) gene during development. We addressed this by identifying MARs and studying their distribution and differentiation, in the posterior silk glands of Bombyx mori during 5th instar development.

Results

Of the MARs identified on three different days, 7.15% MARs were common to all 3 days, whereas, 1.41, 19.27 and 52.47% MARs were unique to day 1, day 5, and day 7, respectively highlighting the dynamic nature of the matrix associated DNA. The average chromatin loop length based on the chromosome wise distribution of MARs and the distances between these MAR regions decreased from day 1 (253.91 kb) to day 5 (73.54 kb) to day 7 (39.19 kb). Further significant changes in the MARs in the vicinity of the FIBH gene were found during different days of 5^th instar development which implied their role in the regulation and expression of the FIBH gene.

Conclusions

The presence of MARs in the flanking regions of genes found to exhibit differential expression during 5^th instar development indicates their possible role in the regulation of their expression. This reiterates the importance of MARs in the genomic functioning as regulators of the molecular mechanisms in the nucleus. This is the first study that takes into account the tissue specific genome-wide MAR association and the potential role of these MARs in developmentally regulated gene expression. The current study lays a foundation to understand the genome wide regulation of chromatin during development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08446-3.

Genetic parameters in traits of productive importance in lines of Bombyx mori L

In the textile industry, complex cocoon traits are closely related to silk production. The aim of the present study was to estimate genetic parameters of economic importance traits-cocoon length (CL), cocoon weight (CW) and shell weight (SW)-in three B. mori lines-Chinese (C6), Japanese (J7) and Indian (C. Nichi)-reared under different temperature and photoperiod conditions. For each of these lines, data were collected from several generations with a full-sibling family structure and variance-covariance component were obtained via restricted maximum likelihood (REML) estimates based on a bi-trait animal model analysed through the multiple-trait derivative-free restricted maximum likelihood (MTDFREML) software. Genetic parameters of the traits varied between the silkworm lines were evaluated. Heritabilities were highest in J7 line (0.71, 0.89 and 0.93 for CL, CW and SW, respectively) followed by C6 (0.48, 0.54 and 0.50 for CL, CW and SW, respectively) and C. Nichi (0.36, 0.43 and 0.40 for CL, CW and SW, respectively). Phenotypic correlations among these lines were positive, with values ranging between 0.36 and 0.767. Similarly, genetic correlations between the analysed silkworm lines were observed to be positive, with high values ranging from 0.86 to 0.94. The evidence for environmental correlation in these lines was found only between CW-SW traits with moderate to high values ranging from 0.600 to 0.940. The magnitude of heritability and genetic correlations implies that phenotypic variations of the CL, CW and SW traits depend mainly on genotypic variation within the J7, C6 and C. Nichi lines, and that simultaneous genetic gains are possible by implementing selection processes for any of the evaluated traits.