Evaluation of Genetic Diversity in Chlorophytum borivilianum (Santp. and Fernan.) Using Molecular Markers: An Endangered Medicinal Plant

Chlorophytum borivilianum is a traditional medicinal plant distributed throughout the tropics and subtropics. In the present investigation, RAPD and ISSR analyses were used to assess the genetic diversity among 21 accessions collected from different geographical regions of India using 20 RAPD primers and 6 ISSR primers. RAPD and ISSR primers revealed 92.26% and 82.76% polymorphism, respectively. Similarity in coefficient values ranged from 0.321 to 0.707 for RAPD and 0.363 to 0.846 for ISSR markers. The dendrogram developed by RAPD and ISSR marker‐based analysis grouped the 21 accessions into different clusters. Mantel test employed for detection of goodness of fit established the cophenetic correlation value for both the primer systems and it was observed to be significant. Clustering of accessions within groups was also similar based on RAPD‐ and ISSR‐derived dendrograms. In our study, both marker systems were similar except for the percentage polymorphism which was found to be greater using RAPD, thus indicating the greater effectiveness of RAPD primers for estimating genetic variation of C. borivilianum

Identification and characterization of polymorphic genic SSR markers between cultivated (Oryza sativa) and Indian wild rice (Oryza nivara)

299-310In the present study, we developed a set of 100 BC2F4 mapping lines derived from the cross between the Oryza nivara (AC100476) and high yielding indica rice, Lalat. Out of 410 RM markers used for polymorphism survey between the parental lines, we identified around 113 (28.9%) polymorphic rice microsatellite (RM) markers between the parental lines that were uniformly distributed among the 12 chromosomes except for few gaps on chromosome 1, 7 and 10. On the basis of motif length, the trinucleotide repeats-motif, (TTA)n was the longest with a maximum motif length of 177 nucleotides. Among the repeat motifs, di-nucleotide repeat-motifs was the most abundant (68.14%) with the motifs (AC/GT)n were the most abundant accounting 56.32% of the total dinucleotide repeat-motifs. Out of the 113 polymorphic RM markers, 56 (49.55%) were found to be genic markers and broadly distributed into three groups such as molecular, biological and cellular categories with 38%, 32% and 30% frequencies, respectively. The present finding would be useful for the identification and mapping of drought related traits and development of drought tolerant rice cultivars in rice breeding program

Analysis of allelic variation of 7 grain regulating genes in 89 germplasm.

<p>Analysis of allelic variation of 7 grain regulating genes in 89 germplasm.</p

Effect of multiple allelic combinations of genes on regulating grain size in rice

<div><p>The grain size is one of the complex trait of rice yield controlled by a plethora of interaction of several genes in different pathways. The present study was undertaken to investigate the influence of seven known grain size regulating genes: <i>DEP1</i>, <i>GS7</i>, <i>GS3</i>, <i>GW8</i>, <i>GL7</i>, <i>GS5</i> and <i>GW2</i>. A wide phenotypic variation for grain length, grain width and grain length-width ratio were observed in 89 germplasm. The correlation analysis showed a strong association among these three grain traits viz. GL, GW, GLWR and TGW which play important roles in determining the final rice grain size. Except for <i>GW2</i>, all six genes showed strong association with grain size traits. A total of 21 alleles were identified with an average of 2.1 allele/locus in 89 germplasm of which seven alleles were found to be favourable alleles for improving the grain size with the frequency range of 24 (26.97%) to 82 (92.13%); the largest was found in <i>GS5</i> followed by <i>GW8</i>, <i>GL7</i>, <i>DEP1</i>, <i>GS3</i> and <i>GS7</i> genes. Through ANOVA, four markers (GS3-<i>Pst</i>I, S9, GID76 and GID711) of three genes (<i>GS3</i>, <i>DEP1</i> and <i>GL7</i>) were found significantly associated with all the three traits (GL, GLWR and TGW). Concurrent results of significant associations of grain size traits with other markers were observed in both analysis of variance and genetic association through the general linear model. Besides, the population structure analysis, cluster analysis and PCoA divided the entire germplasm into three sub-groups with the clear-cut demarcation of long and medium grain types. The present results would help in formulating strategies by selecting suitable candidate markers/genes for obtaining preferred grain shape/size and improving grain yield through marker-assisted breeding.</p></div

Frequency distribution of favourable alleles of six genes related to grain size in 89 rice germplasm.

<p>Frequency distribution of favourable alleles of six genes related to grain size in 89 rice germplasm.</p

Cluster analysis of 89 germplasm based on 7 grain size regulating genes.

<p>Cluster analysis of 89 germplasm based on 7 grain size regulating genes.</p

Details of the 10 molecular markers for 7 grain size regulating genes used in the present studied.

<p>Details of the 10 molecular markers for 7 grain size regulating genes used in the present studied.</p

Pyramiding of favourable alleles of six genes for GL and GLWR.

<p>Pyramiding of favourable alleles of six genes for GL and GLWR.</p

Correlation coefficients analysis among the four traits for grain size.

<p>Correlation coefficients analysis among the four traits for grain size.</p

Descriptive statistics for grain size traits in 89 rice germplasm.

<p>Descriptive statistics for grain size traits in 89 rice germplasm.</p