Identification of simple sequence repeat markers linked to heat tolerance in rice using bulked segregant analysis in F2 population of NERICA-L 44 × Uma.

The damage caused by high temperature is one of the most important abiotic stress affecting rice production. Reproductive stage of rice is highly susceptible to high temperature. The present investigation was undertaken to identify polymorphic microsatellite markers (SSR) associated with heat tolerance. The rice cultivars NERICA- L 44 (heat tolerant) and Uma (heat susceptible) were crossed to generate F1 and F2 populations. The F2 population was subjected to heat stress at >38°C and the 144 F2 plants were evaluated for their tolerance. The results note that the mean of the F2 population was influenced by the tolerant parent with regards to the traits of plant height, membrane stability index, photosynthetic rate, stomatal conductance, evapotranspiration rate, pollen viability, spikelet fertility and 1000 grain weight. Ten each of the extremely susceptible and tolerant plants were selected based on the spikelet fertility percentage. Their DNA was pooled into tolerant and susceptible bulks and Bulked Segregant Analysis (BSA) was carried out using 100 SSR markers to check for polymorphism. The survey revealed a polymorphism of 18% between the parents. RM337, RM10793, RM242, RM5749, RM6100, RM490, RM470, RM473, RM222 and RM556 are some of the prominent markers that were found to be polymorphic between the parents and the bulks. We performed gene annotation and enrichment analysis of identified polymorphic markers. Result revealed that the sequence specific site of that chromosome mostly enriched with biological processes like metabolic pathway, molecular mechanism, and subcellular function. Among that RM337 was newly reported marker for heat tolerance. Expression analysis of two genes corresponds to RM337 revealed that LOP1 (LOC_Os08g01330) was linked to high temperature tolerance in rice. The results demonstrate that BSA using SSR markers is useful in identifying genomic regions that contribute to thermotolerance.

cgSSR marker-based genome-wide association study identified genomic regions for panicle characters and yield in rice (Oryza sativa L.).

BACKGROUND: To improve production efficiency, positive alleles corresponding to yield-related attributes must be accumulated in a single elite background. We designed and used cgSSR markers, which are superior to random SSR markers in genome-wide association study, to identify genomic regions that contribute to panicle characters and grain yield in this study. RESULTS: As evidenced by the high polymorphic information content value and gene diversity coefficient, the new cgSSR markers were determined to be highly informative. These cgSSR markers were employed to generate genotype data for an association panel evaluated for four panicle characters and grain yield over three seasons. For five traits, 17 significant marker-trait associations on six chromosomes were discovered. The percentage of phenotypic variance that could be explained ranged from 4% to 13%. Unrelated gene-derived markers had a strong association with target traits as well. CONCLUSION: Trait-associated cgSSR markers derived from corresponding or related genes ensure their utility in direct allele selection, while other linked markers aid in allele selection indirectly by altering the phenotype of interest. Through a marker-assisted breeding approach, these marker-trait associations can be leveraged to accumulate favourable alleles for yield enhancement in rice. © 2022 Society of Chemical Industry.

A combination of moderate and vigorous physical activities reduces the burden of multimorbidity: findings from Longitudinal Ageing Study in India.

BACKGROUND: Physical inactivity is a significant factor contributing to the prevalence of non-communicable diseases (NCDs). The objective of this study is to examine the association between physical activity and multimorbidity among Indian adults aged 45 years and above by residence. METHODS: Data from Longitudinal Ageing Study in India (LASI) 2017-2018, wave 1, a nationally representative study, are used to examine the above objective. A total of 59,073 adults aged 45 years and above are enlisted in the study. Physical activities and other demographic and socioeconomic variables have been used to describe the distribution of multimorbidity and investigate their relationship. Logistic regression is employed to examine the adjusted impact of physical activity on multimorbidity among Indian adults (45 + years) by residence. RESULTS: The level of physical activity is inversely related to the prevalence of multimorbidity in India. The rate of multimorbidity ranges from 4 to 12% among moderately active individuals in rural areas, whereas it ranges from 9 to 34% in urban areas across the age groups of 45 to 75+ years. Notably, the individuals who engage in both moderate and vigorous activities have a lower prevalence of multimorbidity than those who engage in only moderate activities. CONCLUSION: Our study shows that physical inactivity has an association with the rise in multimorbidity in both rural and urban areas; however, the intensity of multimorbidity is higher in urban areas. The policymakers should consider the influence of moderate and vigorous physical activity as a key prevention measure of non-communicable disease and multimorbidity.

Understanding natural genetic variation for grain phytic acid content and functional marker development for phytic acid-related genes in rice.

BACKGROUND: The nutritional value of rice can be improved by developing varieties with optimum levels of grain phytic acid (PA). Artificial low-PA mutants with impaired PA biosynthesis have been developed in rice through induced mutagenesis. However, low-PA mutant stocks with drastically reduced grain PA content have poor breeding potential, and their use in rice breeding is restricted due to their detrimental pleiotropic effects, which include decreased seed viability, low grain weight, and low seed yield. Therefore, it is necessary to take advantage of the natural variation in grain PA content in order to reduce the PA content to an ideal level without compromising the crop's agronomic performance. Natural genetic diversity in grain PA content has not been thoroughly examined among elite genetic stocks. Additionally, given grain PA content as a quantitative trait driven by polygenes, DNA marker-assisted selection may be required for manipulation of such a trait; however, informative DNA markers for PA content have not yet been identified in rice. Here we investigated and dissected natural genetic variation and genetic variability components for grain PA content in rice varieties cultivated in Eastern and North-Eastern India during the last 50 years. We developed novel gene-based markers for the low-PA-related candidate genes in rice germplasm, and their allelic diversity and association with natural variation in grain PA content were studied. RESULTS: A wide (0.3-2.8%), significant variation for grain PA content, with decade-wise and ecology-wise differences, was observed among rice varieties. Significant genotype x environment interaction suggested polygenic inheritance. The novel candidate gene-based markers detected 43 alleles in the rice varieties. The new markers were found highly informative as indicated by PIC values (0.11-0.65; average: 0.34) and coverage of total diversity. Marker alleles developed from two putative transporter genes viz., SPDT and OsPT8 were significantly associated with grain PA variation assayed on the panel. A 201 bp allele at the 3' UTR of SPDT gene was negatively associated with grain PA content and explained 7.84% of the phenotypic variation. A rare allele in the coding sequence of OsPT8 gene was positively associated with grain PA content which explained phenotypic variation of 18.49%. CONCLUSION: Natural variation in grain PA content is substantial and is mostly controlled by genetic factors. The unique DNA markers linked with PA content have significant potential as genomic resources for the development of low-PA rice varieties through genomics-assisted breeding procedures.

Unravelling genetic architecture and development of core set from elite rice lines using yield-related candidate gene markers.

Assessing genetic diversity and development of a core set of elite breeding lines is a prerequisite for selective hybridization programes intended to improve the yield potential in rice. In the present study, the genetic diversity of newly developed elite lines derived from indicax tropical japonica and indicax indica crosses were estimated by 38 reported molecular markers. The markers used in the study consist of 24 gene-based and 14 random markers related to grain yield-related QTLs distributed across the rice genome. Genotypic characterization was carried out to determine the genetic similarities between the elite lines. In total, 75 alleles were found using 38 polymorphic markers, with polymorphism information content ranging from 0.10 to 0.51 with an average of 0.35. The genotypes were divided into three groups based on cluster analysis, structure analysis and also dispersed throughout the quadrangle of PCA, but nitrogen responsive lines clustered in one quadrangle. Seven markers (GS3_RGS1, GS3_RGS2, GS5_Indel1, Ghd 7_05SNP, RM 12289, RM 23065 and RM 25457) exhibited PIC values ≥ 0.50 indicating that they were effective in detecting genetic relationships among elite rice. Additionally, a core set of 11 elite lines was made from 96 lines in order to downsize the diversity of the original population into a small set for parental selection. In general, the genetic information collected in this work will aid in the study of grain yield traits at molecular level for other sets of rice genotypes and for selecting diverse elite lines to develop a strong crossing programme in rice. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01190-8.

Understanding complex genetic architecture of rice grain weight through QTL-meta analysis and candidate gene identification.

Quantitative trait loci (QTL) for rice grain weight identified using bi-parental populations in various environments were found inconsistent and have a modest role in marker assisted breeding and map-based cloning programs. Thus, the identification of a consistent consensus QTL region across populations is critical to deploy in marker aided breeding programs. Using the QTL meta-analysis technique, we collated rice grain weight QTL information from numerous studies done across populations and in diverse environments to find constitutive QTL for grain weight. Using information from 114 original QTL in meta-analysis, we discovered three significant Meta-QTL (MQTL) for grain weight on chromosome 3. According to gene ontology, these three MQTL have 179 genes, 25 of which have roles in developmental functions. Amino acid sequence BLAST of these genes indicated their orthologue conservation among core cereals with similar functions. MQTL3.1 includes the OsAPX1, PDIL, SAUR, and OsASN1 genes, which are involved in grain development and have been discovered to play a key role in asparagine biosynthesis and metabolism, which is crucial for source-sink regulation. Five potential candidate genes were identified and their expression analysis indicated a significant role in early grain development. The gene sequence information retrieved from the 3 K rice genome project revealed the deletion of six bases coding for serine and alanine in the last exon of OsASN1 led to an interruption in the synthesis of α-helix of the protein, which negatively affected the asparagine biosynthesis pathway in the low grain weight genotypes. Further, the MQTL3.1 was validated using linked marker RM7197 on a set of genotypes with extreme phenotypes. MQTL that have been identified and validated in our study have significant scope in MAS breeding and map-based cloning programs for improving rice grain weight.

Uneven economic burden of non-communicable diseases among Indian households: A comparative analysis.

BACKGROUND: Non-communicable diseases (NCDs) are the leading global cause of death and disproportionately concentrate among those living in low-income and middle-income countries. However, its economic impact on households remains less well known in the Indian context. This study aims to assess the economic impact of NCDs in terms of out-of-pocket expenditure (OOPE) and its catastrophic impact on NCDs affected households in India. MATERIALS AND METHODS: Data were collected from the 75th round of the National Sample Survey Office, Government of India, conducted in the year 2017-18. This is the latest round of data available on health, which constitutes a sample of 113,823 households. The collection of data is based on a stratified multi-stage sampling method. Generalised Linear Regression model was employed to identify the socio-economic covariates associated with the catastrophic health expenditure (CHE) on hospitalisation. RESULTS: The result shows a higher burden of OOPE on NCDs affected households. The mean expenditure by NCDs households in public hospitals is INR 13,170 which is more than twice as compared to the non-NCDs households INR 6,245. Particularly, the proportion of total medical expenditure incurred on medicines (0.39) and diagnostics (0.15) is troublesome for households with NCDs, treated in public hospitals. Moreover, results from the generalised linear regression model confirm the significant relationship between CHE with residence, caste, religion, household size, and economic status of households. The intensity of CHE is more for the households who are poor, drinking unsafe water, using firewood as cooking fuel, and household size of 1-5 members. CONCLUSION: Therefore, an urgent need for a prevention strategy should be made by the government to protect households from the economic burden of NCDs. Specifically, to reduce the burden of CHE associated with NCDs, a customised disease-specific health insurance package should be introduced by the government of India in both public and private facilities.

A single nucleotide substitution in the SPDT transporter gene reduced phytic acid and increased mineral bioavailability from Rice grain (Oryza sativa L.).

Phosphorus (P) flow in agricultural land depends on the P taken off from harvested product, its losses through runoff and fertilizer applied to balance the removed P. Phytic acid (PA), the major storage form of phosphorus (P) in cereal grains is a key anti-nutrient for human and non-ruminants leads to eutrophication of waterways. As the natural non-renewable P reserves are limited, enhancing P use efficiency is needed for field crops. SULTR-like phosphorus distribution transporter (SPDT) is a novel rice transporter transfer P to the grain. Any alteration in transporter gene reduce grain P with concomitant rise in the leaves. A low PA (3.0 g/kg) rice Khira was identified where a single nucleotide mutation in LOC_Os06g05160 gene encoding SPDT showed low P transportation to grain. An amino acid change was detected as Valine-330 to Alanine at the 3' end of fifth exon. Highest expression of SPDT was observed in node I of rice as compared to low PA genotype. The mutation in SPDT could significantly affect P and PA accumulation in the grains with increased mineral bioavailability. PRACTICAL APPLICATIONS: Excessive P application in crop leads to higher production cost as well as rapid depletion of limited rock phosphate. Alteration of P transporter function in the rice lower PA and total P accumulation in the grains with increased mineral bioavailability. The re-distributed P in the straw can be applied as manure to the rice field. Thus, less P will be removed from the field, result in the decreased requirement for P fertilizer.

Does choice of health care facility matter? Assessing out-of-pocket expenditure and catastrophic spending on emergency obstetric care in India.

The key recommendation of the Child Survival and Safe Motherhood programme was the provision of Emergency Obstetric Care (EmOC) for the prevention of maternal mortality, especially in developing countries like India. The objectives of this paper were three-fold: to examine the socioeconomic differentials in mean out-of-pocket expenditure on EmOC in public and private health care facilities in India; to evaluate the catastrophic health expenditure of households at the threshold levels of 5% and 10%; and finally, to assess the effects of various socioeconomic and demographic covariates on the levels of catastrophic health expenditure on EmOC. Data were extracted from the 71st round of the National Sample Survey Office (NSSO) survey conducted in India between January and June 2014. A stratified multi-stage sampling design was followed to conduct the survey. The information was collected from 65,932 households (rural: 36,480; urban: 29,452) and 33,104 individuals across various states and union territories in India. However, the present study had taken only 1653 sample women who availed EmOC care during the last one year preceding the survey date. Binary logistic regression was applied. Large differences in out-of-pocket expenditure on EmOC were found between private and public health care facilities. Mean annual out-of-pocket expenditure by women in private hospitals was INR 23,309 (US$367), which was about 6 times higher than in public hospitals, where mean spending was INR 3651 (US$58). Furthermore, logistic regression analysis showed a significant association between household socioeconomic status and level of catastrophic health expenditure on EmOC. The odds of catastrophic health expenditure in public health facilities among women from the North region were higher than among those from the Central, South and West regions. Age and level of education significantly influenced the mean level of catastrophic health expenditure. Access to good-quality obstetric care is key to reducing the maternal mortality rate and child deaths, and thus achieving Sustainable Development Goal 3. There is an urgent need for policy interventions to reduce the financial burden of households in accessing obstetric care in India.