Variability Assessment for Root and Drought Tolerance Traits and Genetic Diversity Analysis of Rice Germplasm using SSR Markers

The studies on genetic variation, diversity and population structure of rice germplasm of North East India could be an important step for improvements of abiotic and biotic stress tolerance in rice. Genetic diversity and genetic relatedness among 114 rice genotypes of North East India were assessed using genotypic data of 65 SSR markers and phenotypic data. The phenotypic diversity analysis showed the considerable variation across genotypes for root, shoot and drought tolerance traits. The principal component analysis (PCA) revealed the fresh shoot weight, root volume, dry shoot weight, fresh root weight and drought score as a major contributor to diversity. Genotyping of 114 rice genotypes using 65 SSR markers detected 147 alleles with the average polymorphic information content (PIC) value of 0.51. Population structure analysis using the Bayesian clustering model approach, distance-based neighbor-joining cluster and principal coordinate analysis using genotypic data grouped the accession into three sub-populations. Population structure analysis revealed that rice accession was moderately structured based on FST value estimates. Analysis of molecular variance (AMOVA) and pairwise FST values showed significant differentiation among all the pairs of sub-population ranging from 0.152 to 0.222 suggesting that all the three subpopulations were significantly different from each other. AMOVA revealed that most of the variation in rice accession mainly occurred among individuals. The present study suggests that diverse germplasm of NE India could be used for the improvement of root and drought tolerance in rice breeding programmes.

Physical characterization of the homoeologous Group 5 chromosomes of wheat in terms of rice linkage blocks, and physical mapping of some important genes

The wheat homoeologous Group 5 chromosomes were characterized physically in terms of rice linkage blocks using a deletion mapping approach. All three chromosomes, 5A, 5B, and 5D, were shown to have a similar structure, apart from the 4A-5A translocation on the distal end of chromosome arm 5AL. The physical mapping of rice markers on the deletion lines revealed that the whole of rice chromosome 9 is syntenous to a large block, proximal to the centromere, on the long arm. Likewise, a small segment of the distal end of the long arm showed conserved synteny with the distal one-third end of the long arm of rice chromosome 3. In between those conserved regions, there is a region on the long arm of the Group 5 chromosomes which shows broken synteny. The proximal part of the short arms of the Group 5 chromosomes showed conserved synteny with a segment of the short arm of rice chromosome 11 and the distal ends showed conserved synteny with a segment of rice chromosome 12. The physical locations of flowering time genes (Vrn and earliness per se) and the gene for grain hardness (Ha) on the Group 5 chromosomes were determined. These results indicate that comparative mapping using the deletion mapping approach is useful in the study of genome relationships, the physical location of genes, and can determine the appropriate gene cloning strategy. Key words: wheat, rice, comparative mapping, deletion lines.

Genetic gains in forage sorghum for adaptive traits for non - conventional area through multi-trait-based stability selection methods

Introduction

In the Asian tropics, unpredictable weather increases the risk of abiotic stresses in sorghum areas, making it harder to meet predicted demand. Genotype-by environment interaction (GEI) and the lack of an effective multi-trait-based selection approach make it challenging to breed climateresilient forage sorghum that adapts to nonconventional areas.

Methods

The present investigation carried out to estimate genetic parameters, inter trait associations, genetic gain under selection (SGs) of 95 diverse forage sorghum genotypes. Fourteen forage yield and other secondary traits were evaluated at five different growing seasons at two locations. Negative and positive genetic gains under selection were estimated across different growing seasons including Kharif, Rabi and Summer in the year 2020 and 2021.

Results and discussion

The GEI effects were significant (P < 0.001) for all the studied traits. The multi trait based stability indices have been said to assist breeders in ensuring sustained progress in primary traits likeforage yield without sacrificing genetic advancement in secondary traits. Fourteen genotypes were selected through each evaluation methods including genotype - ideotype distance index (MGIDI), multi-trait stability index (MTSI), multi-trait stability and mean performance (MTMPS) and multi-trait index based on factor analysis and genotype-ideotype distance (FAIBLUP Index), assuming 15% selection intensity. According to MGIDI, the selected genotypes exhibited desired positive genetic gains for dry forage yield per plant, inter-nodal length, green forage yield per plant, and plant height and negative genetic gains for days to 50% flowering. The strength and weakness plot is a potential graphical tool as portrayed by MGIDI, to identify and develop desirable genotype for particular environment. Two genotypes, G36 (302B) and G89 (348B) were found to be common across all four evaluation methods based on all the studied traits.

Background

Multi-trait stability evaluation approaches are reliable and accessible for selecting multiple traits under varied testing environments with low multicollinearity issues. These tools proved effective in enhancing selection strategies and optimising breeding schemes for the development of climate-resilient forage sorghum genotypes. The aforementioned genotypes were found to be the most reliable, high-yielding, and earlymaturing and could be suggested for variety and hybrid development and ideotype breeding programmes to ensure the food and nutritional security.

Identifying genetic determinants of forage sorghum [Sorghum bicolor (Moench)] adaptation through GWAS

BACKGROUND

Forage sorghum is a highly valued crop in livestock feed production due to its versatility, adaptability, high productivity, and resilience under adverse environmental conditions, making it a crucial option for sustainable forage production. This study aimed to investigate ninety-five forage sorghum genotypes and identify the marker - trait associations (MTAs) in adaptive traits, including yield and flowering through genome-wide association studies (GWAS).

RESULTS

Using 41,854 polymorphic SNPs, a GWAS involving the GLM, MLM, and FarmCPU models was performed to analyse fourteen adaptive traits. The population structure revealed the presence of two subpopulation groups. Linkage disequilibrium (LD) plots showed varying degrees of LD decay across the chromosomes, with an average LD decay of 19.49 kbp. Twelve common significant QTNs, encoding 17 putative candidate genes, were simultaneously co-detected and studied by at least two or more GWAS methods. Three QTNs were associated to days to 50% flowering; two each to leaf-to-stem ratio and number of nodes per plant; and one each to plant height, leaf width, number of leaves per plant, stem girth, and internodal length. Six candidate genes were associated with days to 50% flowering, two each with leaf width, stem girth, leaf-to-stem ratio, and number of nodes per plant, and one each with plant height, number of leaves per plant, and internodal length.

CONCLUSION

FarmCPU was identified as the most suitable and effective among all the models for controlling both false positives and false negatives. Further in-depth analysis of the newly discovered QTNs may lead to the identification of new candidate genes for the trait of interest. These studies elucidate gene functions and could transform forage sorghum breeding through marker-assisted selection and transgenic approaches, accelerating the development of superior forage sorghum varieties and enhancing global food security.

Physical characterization of the homoeologous group 5 chromosomes of wheat in terms of rice linkage blocks, and physical mapping of some important genes

The wheat homoeologous Group 5 chromosomes were characterized physically in terms of rice linkage blocks using a deletion mapping approach. All three chromosomes, 5A, 5B, and 5D, were shown to have a similar structure, apart from the 4A-5A translocation on the distal end of chromosome arm 5AL. The physical mapping of rice markers on the deletion lines revealed that the whole of rice chromosome 9 is syntenous to a large block, proximal to the centromere, on the long arm. Likewise, a small segment of the distal end of the long arm showed conserved synteny with the distal one-third end of the long arm of rice chromosome 3. In between those conserved regions, there is a region on the long arm of the Group 5 chromosomes which shows broken synteny. The proximal part of the short arms of the Group 5 chromosomes showed conserved synteny with a segment of the short arm of rice chromosome 11 and the distal ends showed conserved synteny with a segment of rice chromosome 12. The physical locations of flowering time genes (Vrn and earliness per se) and the gene for grain hardness (Ha) on the Group 5 chromosomes were determined. These results indicate that comparative mapping using the deletion mapping approach is useful in the study of genome relationships, the physical location of genes, and can determine the appropriate gene cloning strategy.

Grain iron and zinc content is independent of anthocyanin accumulation in pigmented rice genotypes of Northeast region of India

The traditional rice genotypes of Assam are considered to have biological value due to the presence of several bioactive compounds like flavonoids, polyphenols, and anthocyanins, which have antioxidant, anti-cancer, anti-diabetic, and anti-aging properties. The pigmented genotypes are considered to have high iron (Fe) content. However, the effect of Fe and Zinc (Zn) accumulation on anthocyanin content is yet to be studied in pigmented rice of Assam. We studied the Fe, Zn, and anthocyanin content in grains of 204 traditional rice of Assam, which are traditionally preferred for their nutraceutical properties. We performed phenotypic and biochemical compositional analyses of 204 genotypes to identify those having high Fe, Zn, and anthocyanin. We also carried out the differential expression of a few selected Fe and Zn transporter genes along with the expression of anthocyanin biosynthesis genes. Interestingly, all pigmented rice genotypes contained a higher amount of phenolic compound than the non-pigmented form of rice. We found the highest (32.73 g) seed yield per plant for genotype Jengoni followed by Kajoli chokuwa and Khau Pakhi 1. We also listed 30 genotypes having high levels of Fe and Zn content. The genotype Jengoni accumulated the highest (186.9 μg g-1) Fe, while the highest Zn (119.9 μg g-1) content was measured in genotype Bora (Nagaon), The levels of Ferritin 2 gene expression were found to be significantly higher in Bora (Nagaon) (> 2-fold). For Zn accumulation, the genotype DRR Dhan-45, which was released as a high Zn content variety, showed significant up-regulation of the ZIP4 gene at booting (> 7-fold), post-anthesis (7.8-fold) and grain filling (> 5-fold) stages followed by Bora (Nagaon) (> 3-fold) at post-anthesis. Anthocyanidin synthase gene, Flavanone 3-dioxygenase 1-like (FDO1), and Chalcone-flavanone isomerase-like genes were up-regulated in highly pigmented genotype Bora (Nagaon) followed by Jengoni. Based on our data there was no significant correlation between iron and zinc content on the accumulation of anthocyanin. This challenges the present perception of the higher nutritive value in terms of the micronutrient content of the colored rice of Assam. This is the first report on the detailed characterization of traditional rice genotypes inclusive of phenotypic, biochemical, nutritional, and molecular attributes, which would be useful for designing the breeding program to improve Fe, Zn, or anthocyanin content in rice.