Identification of Restorers and Maintainers for Development of Rice Hybrids using WA and Kalinga sources of CMS lines

Three cytoplasmic male sterile (CMS) lines of rice having wild abortive (WA) and Kalinga cytoplasmic male sterility source were crossed with seven testers to identify their restorer/maintainer nature. Total of 21 hybrids were subjected to pollen and spikelet fertility analysis along with their parents. Most of the genotypes expressed differential fertility reactions when crossed with CMS lines were identifies as potential restorers. None of the genotypes identified as potential maintainer based on pollen and spikelet fertility. Among these, Bagdidhan was identified as restorer for all three cms lines. Potential restorers identified in the present investigation could be used to develop good, high yielding and promising rice hybrids

Gene action and combining ability analyses to develop NPT based rice hybrids in Chhattisgarh plains

Combining ability in New Plant Type (NPT) lines of rice for hybrid rice breeding programme has been carried out in line x tester mating design involving 3 CMS lines and 6 testers. The analysis of variance for combining ability of all the traits showed that variances due to treatments, parents, hybrids were highly significant. The analysis further revealed highly significant differences for all the characters among the lines, testers and line X tester and parents’ vs hybrids. Among the CMS lines IR 58025A was identified as a good general combiner for grain yield per plant. Among the testers NPT line HR 703 (3.09) was found to be good combiner for grain yield per plant followed by Jirashankar (NPT-Sel) (2.36) and IIRON N-1-114(0.79). The significant difference between lines x tester interaction indicates that SCA attributed heavily in the expression of these traits and demonstrates the importance of dominance or non additive variances for all the traits. Three crosses viz., IR 58025A/HR 703, IR 79156A/IIRON N-1-114, and CRMS 31A /PAU1196 were identified as most promising based on SCA effects, better per se performance and both the parents with high or low GCA effects

InDel marker based genetic differentiation and genetic diversity in traditional rice (Oryza sativa L.) landraces of Chhattisgarh, India.

Rice has been cultivating and utilizing by humans for thousands of years under diverse environmental conditions. Therefore, tremendous genetic differentiation and diversity has occurred at various agro-ecosystems. The significant indica-japonica differentiation in rice provides great opportunities for its genetic improvement. In the present investigation, a total of 42 polymorphic InDel markers were used for differentiating 188 rice landraces and two local varieties of Chhattisgarh, India into indica and japonica related genotypes based on 'InDel molecular index'. Frequency of japonica alleles varied from 0.11 to 0.89 among landraces. Results revealed that 104 rice landraces have indica type genetic architecture along with three tested indica cultivars Swarna, Mahamaya and Rajeshwari. Another 60 landraces were placed under 'close to indica' type. It was found that three rice landraces i.e. Kalajeera, Kapri, Tulsimala were 'close to japonica' type and 21 landraces were 'intermediate' type. The result from the calculation of 'InDel molecular index' was further verified with STRUCTURE, AMOVA, PCA and cluster analysis. Population structure analysis revealed two genetically distinct populations within the 190 rice landraces/genotypes. Based on AMOVA, 'intermediate' type, 'close to japonica' type and Dongjinbyeo (a japonica cultivar from Republic of Korea) displayed significant genetic differentiation (ɸPT = 0.642, P = 0.000) from 'indica' and 'close to indica' groups. The PCA scatter plot and dendrogram demonstrated a clear pattern of two major group differentiations. 'Close to japonica' type and 'intermediate' type landraces/genotypes were grouped with Dongjinbyeo and formed a separate cluster at 30% Jaccard's similarity level from rest of the landraces/genotypes which were 'close to indica' or 'indica' type. Such a significant genetic differentiation among the locally adapted landraces could be exploited for the development of rice varieties introgressing higher yield potential and better plant types of japonica type as per the need of consumers and rice traders

Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review

The recent advancements in forward genetics have expanded the applications of mutation techniques in advanced genetics and genomics, ahead of direct use in breeding programs. The advent of next-generation sequencing (NGS) has enabled easy identification and mapping of causal mutations within a short period and at relatively low cost. Identifying the genetic mutations and genes that underlie phenotypic changes is essential for understanding a wide variety of biological functions. To accelerate the mutation mapping for crop improvement, several high-throughput and novel NGS based forward genetic approaches have been developed and applied in various crops. These techniques are highly efficient in crop plants, as it is relatively easy to grow and screen thousands of individuals. These approaches have improved the resolution in quantitative trait loci (QTL) position/point mutations and assisted in determining the functional causative variations in genes. To be successful in the interpretation of NGS data, bioinformatics computational methods are critical elements in delivering accurate assembly, alignment, and variant detection. Numerous bioinformatics tools/pipelines have been developed for such analysis. This article intends to review the recent advances in NGS based forward genetic approaches to identify and map the causal mutations in the crop genomes. The article also highlights the available bioinformatics tools/pipelines for reducing the complexity of NGS data and delivering the concluding outcomes

Analysis of molecular variance between proposed ‘indica’/’close to indica’ and ‘close to japonica’/’intermediate’ populations of rice landraces from Chhattisgarh, India.

<p>Analysis of molecular variance between proposed ‘indica’/’close to indica’ and ‘close to japonica’/’intermediate’ populations of rice landraces from Chhattisgarh, India.</p

Classification of rice landraces into <i>indica</i> or <i>japonica</i> types based on the ‘InDel Molecular Index’.

<p>Classification of rice landraces into <i>indica</i> or <i>japonica</i> types based on the ‘InDel Molecular Index’.</p

Details of InDel markers used in the present investigation.

<p>Details of InDel markers used in the present investigation.</p

Population structure of traditional rice landraces of Chhattisgarh, India based on model-based clustering using STRUCTURE.

<p>Population structure of traditional rice landraces of Chhattisgarh, India based on model-based clustering using STRUCTURE.</p

Genetic differentiation of 192 rice landraces/genotypes from Chhattisgarh, India based on principle component analysis.

<p>Note: Blue diamond represents rice genotypes that include Dongjinbyeo, ‘close to <i>japonica</i>’ and ‘intermediate’ type of landraces. Red circle represents remaining ‘intermediate’ type of landraces which have more <i>indica</i> allele. The black circle represents all the ‘<i>indica</i>’ and ‘close to <i>indica</i>’ type of rice landraces including Swarna, Mahamaya and Rajeshwari varieties.</p

Pictorial map of collection sites of 190 rice landraces/genotypes from Chhattisgarh states in India.

<p>Note: The map was downloaded from <a href="https://upload.wikimedia.org/wikipedia/commons/7/79/India_Chhattisgarh_locator_map.svg" target="_blank">https://upload.wikimedia.org/wikipedia/commons/7/79/India_Chhattisgarh_locator_map.svg</a> and was reproduced here with due permission from the curator (Courtesy to <a href="mailto:[email protected]" target="_blank">[email protected]</a>).</p