Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits.

The aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181 aus accessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits.Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identified OsSAC1 on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance of OsGLT1 and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations in aus rice.In summary, this study offers valuable insights into the genetic structure and phenotypic diversity of aus rice accessions. We have identified significant loci associated with essential agronomic traits, with GLT1, PUP4, and SAC1 genes emerging as key players in yield determination.

Capturing Genetic Variability and Identification of Promising Drought-Tolerant Lines in Exotic Landrace Derived Population Under Reproductive Drought Stress in Rice.

Drought is one of the most predominant abiotic stresses in this century, leading to a drastic reduction in the yield of rainfed rice ecosystems. Breeding of drought-resilient rice varieties is very much in demand for sustainable rice production in drought-prone rainfed ecology. An experiment was designed under irrigated non-stress and drought-stress situations involving an exotic drought-tolerant landrace (Chao Khaw) and a high-yielding aromatic rice cultivar (Kasturi), and an F2:4 derived population of 156 breeding lines was developed at IRRI South Asia Hub, Hyderabad. The objective of the study was to assess the genetic variability, drought tolerance behavior, and identify promising breeding lines for different rice ecologies and drought breeding programs. Restricted maximum likelihood (REML) analysis using the mixed model approach revealed a considerable genetic variation in the population for yield and yield contributing traits in non-stress and drought-stress conditions. We observed very high heritability for all the selected traits under stress 2015 WS (73.8% to 85.3%) and 2016 WS (72.4% to 93.5%) and non-stress 2015 WS (68.2% To 92.9%) and 2016 WS (61.4% to 92.6%) environments, indicating possible selection for grain yield under drought stress and non-stress with the same precision level. None of the secondary traits except harvest index and biomass included in our study showed a positive association with grain yield, indicating indirect selection's ineffectiveness in improving yield under drought. A total of 48 promising breeding lines were found to have a better yield than donor Chao Khaw (up to 38% advantage) and popular drought-tolerant cultivars Shabhagidhan (up to 48% advantage) in stress conditions and recommended for rainfed upland ecology, 34 breeding lines under the well-watered condition suited for rainfed lowland ecology. Overall, the study found 21 common breeding lines that showed their superiority in non-stress and under drought stress situations, fitting best in rainfed lowland ecology with occasional drought occurrence. The large genetic variation found in this population can be exploited further to develop a few forward breeding high-yielding lines with better drought tolerance ability and used as drought donors in drought breeding programs.

High efficient de novo root-to-shoot organogenesis in Citrus jambhiri Lush.: Gene expression, genetic stability and virus indexing.

A protocol for high-frequency direct organogenesis from root explants of Kachai lemon (Citrus jambhiri Lush.) was developed. Full-length roots (~3 cm) were isolated from the in vitro grown seedlings and cultured on Murashige and Skoog basal medium supplemented with Nitsch vitamin (MSN) with different concentrations of cytokinin [6-benzylaminopurine, (BAP)] and gibberellic acid (GA3). The frequency of multiple shoot proliferation was very high, with an average of 34.3 shoots per root explant when inoculated on the MSN medium supplemented with BAP (1.0 mg L-1) and GA3 (1.0 mg L-1). Optimal rooting was induced in the plantlets under half strength MSN medium supplemented with indole-3-acetic acid (IAA, 0.5-1.0 mg L-1). IAA induced better root structure than 1-naphthaleneacetic acid (NAA), which was evident from the scanning electron microscopy (SEM). The expressions of growth regulating factor genes (GRF1 and GRF5) and GA3 signaling genes (GA2OX1 and KO1) were elevated in the regenerants obtained from MSN+BAP (1.0 mg L-1)+GA3 (1.0 mg L-1). The expressions of auxin regulating genes were high in roots obtained in ½ MSN+IAA 1.0 mg L-1. Furthermore, indexing of the regenerants confirmed that there was no amplicons detected for Huanglongbing bacterium and Citrus tristeza virus. Random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers detected no polymorphic bands amongst the regenerated plants. This is the first report that describes direct organogenesis from the root explant of Citrus jambhiri Lush. The high-frequency direct regeneration protocol in the present study provides an enormous significance in Citrus organogenesis, its commercial cultivation and genetic conservation.

Population structure and association analysis of heat stress relevant traits in chickpea (Cicer arietinum L.).

Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.