The comparison of inter simple sequence repeat and randomly amplified polymorphic DNA markers for genetic assessment of intra-specific cotton hybrid genotypes

Abstract Hybridization is one of the main strategies in cotton breeding producing new genotypes and increasing the genetic diversity in the cotton germplasm available. Thirty RAPD and ten ISSR markers were use to assess the genetic diversity in F2 progenies of tetraploid cotton hybri

Simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) analyses of genetic diversity in tissue culture regenerated plants of cotton

Cotton is one of the main economic crop plants of Iran cultivated under continuous artificial selection and cultivation which may lead to genetic erosion and possible loss of useful genetic loci resulting in vulnerability to pests and diseases. For this reason increasing and improving the amount of genetic diversity in cotton germplasm through tissue culture is important. The present report considers genetic diversity induced in tissue culture regenerated plants of three cotton cultivars namely Mehr, Sindose and their hybrid Mehr X Sindose. Surface of seeds were disinfected with 70% ethanol for 2 min and then treated with 5% hypochlorite solution for 20 min. Finally, they were washed 3 to 4 times with sterile distilled water and inoculated aseptically on Murashige and Skoog (MS) basal medium free hormones. Single nodes resulted from seedlings cultured as explants. Inter simple sequence repeat (ISSR) and simple sequence repeat (SSR) primers used produced different number of bands in the genotypes studied showing different levels of molecular polymorphisms in each cultivar. Some common and few specific ISSR/SSR loci were indentified while some bands were present in all the genotypes except one indicating genetic changes in them. Analysis of molecular variance (AMOVA) test showed significant difference (p < 0.05) for ISSR markers but not for SSR markers. Molecular trees obtained showed genetic variations among the regenerated plants of each cultivar due to tissue culture.Keywords: Cotton, genetic diversity, ISSR, RAP

Cribado genético de cultivares diploides y tetraploides de algodón, basado en marcadores de polimorfismo de microsatélites en retrotransposones amplificados (REMAP)

Abstract Continuous artificial selection and cultivation of cultivars has led to genetic erosion and loss of useful genetic loci from the available germplasm. The objective was to evaluate diploid and tetraploid cottons cultivars with REMAP. Low genetic variability within each cultivar was observed, but a high genetic variability occurred within each species (18-68%). AMOVA test revealed 63% of total genetic variability occurred due to among species genetic difference. Unique alleles were detected in the studied species, that can be used for species discrimination. REMAPs could efficiently discriminate the studied diploid from tetraploid species and may be useful for fast screening, as genetic fingerprinting of large cotton germplasm and for planning future hybridization programs.Resumen: La selección artificial continuada y el uso de variedades ha llevado a erosión genética y pérdida de loci genéticos del germoplasma disponible. El objetivo fue evaluar variedades diploides y tetraploides de algodón por REMAP. Se observó baja variabilidad gené- tica dentro de cada variedad, pero alta dentro de cada especie (18- 68%). El AMOVA reveló que el 63% de la variabilidad genética total se produjo debido a diferencia entre especies. Se detectaron alelos únicos en las especies estudiadas, que pueden ser empleados para discriminación. REMAP podrían discriminar eficazmente las especies diploides de las tetraploides y ser últiles para el cribado rápido, actuar como huella genética del gran germoplasma de algodón y para la planificación de programas de hibridadción

Additional file 1 of Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.)

Additional file 1: Table S1. Mean of mid and better parent heterosis observed for yield traits in two location and two-year field experimentation. Table S2. Statistics of RNA sequencing data production. Table S3. Overlapping differentially expressed genes among the in MH, SM, and 1DPA in hybrid. Table S4. Statistics of small RNA sequencing data production. Table S5.  Number of the non-additively expressed genes had siRNA clusters in coding regions or 2kb flanking regions in MH, SM, and 1DPA. Table S6a. List of known differentially expressed miRNA in F1 and its Parents. S6b. List of target prediction of known miRNAs. S6c. List of target prediction of novel miRNAs. Table S7. Alignment summary statistics of whole-genome bisulfite sequencing (WGBS). Table S8. List of common DMRs among parental lines and hybrids. Table S9. Association of DMRs and sRNA among hybrid and its parental lines. Table S10. REVIGO combines the biological process GO with hybrid MPV DEGs. The unified terms of REVIGO GO are organized by major groups. To make understanding the data even easier, clusters are grouped into "main clusters" with broad categories. Table S11. Details of the primers used to validate RNA-seq and bisulfite sequencing data