CRP 2020 Reviews:Rice Agri-Food Systems (RICE)

In 2020 the CGIAR CAS Secretariat is conducting independent reviews of the 12 CGIAR Research Programs (CRPs), including this one of RICE. The reviews will provide information on quality of science and effectiveness in each CRP. This review covers the Phase II years of 2017 through 2019, with a view to identifying lessons for future research modalities

Genomic tools in pearl millet breeding for drought tolerance:Status and prospects

Pearl millet (Penisetum glaucum (L) R. Br.) is a hardy cereal crop grown in the arid and semiarid tropics where other cereals are likely to fail to produce economic yields due to drought and heat stresses. Adaptive evolution, a form of natural selection shaped the crop to grow and yield satisfactorily with limited moisture supply or under periodic water deficits in the soil. Drought tolerance is a complex polygenic trait that various morphological and physiological responses are controlled by hundreds of genes and significantly influenced by the environment. The development of genomic tools will have enormous potential to improve the efficiency and precision of conventional breeding. The apparent independent domestication events, highly outcrossing nature and traditional cultivation in stressful environments maintained tremendous amount of polymorphism in pearl millet. This high polymorphism of the crop has been revealed by genome mapping that in turn stimulated the mapping and tagging of genomic regions controlling important traits such as drought tolerance. Mapping of a major QTL for terminal drought tolerance in independent populations envisaged the prospect for the development of molecular breeding in pearl millet. To accelerate genetic gains for drought tolerance targeted novel approaches such as establishment of marker-trait associations, genomic selection tools, genome sequence and genotyping-by-sequencing are still limited. Development and application of high throughput genomic tools need to be intensified to improve the breeding efficiency of pearl millet to minimize the impact of climate change on its production

Childhood retroperitoneal teratomas: 5 years of experience in a tertiary-care hospital

Background Retroperitoneal teratomas are rare paediatric neoplasms. One should be well versed with the presenting features, relationship with surrounding vital organs and the extent of tumour before operating.Aim The present study was planned to highlight the presenting symptoms, preoperative investigatory findings, intraoperative findings, follow-up protocol and the surgeons’ experience in handling these huge tumours.Setting and design This was a retrospective, tertiary-care hospital-based study.Patients and methods Patients with retroperitoneal teratomas operated between 2010 and 2015 were studied in detail. All the data were collected from case files.Results During the mentioned period, there were seven patients including four males and three females. There was no side predilection (three right, two midline, one left and one lesser omentum). All the tumours were completely excised, and histopathology confirmed the benign nature in all cases. All patients were followed-up with postoperative ultrasound and were found to be normal.Conclusion Retroperitoneal teratomas are benign tumours, and complete excision is curative

Metabolite Diversity and Metabolic Genome-Wide Marker Association Studies (Mgwas) for Health Benefiting Nutritional Traits in Pearl Millet Grains

As efforts are made to increase food security, millets are gaining increasing importance due to their excellent nutritional credentials. Among the millets, pearl millet is the predominant species possessing several health benefiting nutritional traits in its grain that are helpful in mitigating chronic illnesses such as type−2 diabetes and obesity. In this paper, we conducted metabolomic fingerprinting of 197 pearl millet inbred lines drawn randomly from within the world collection of pearl millet germplasm and report the extent of genetic variation for health benefitting metabolites in these genotypes. Metabolites were extracted from seeds and assessed using flow infusion high-resolution mass spectrometry (FIE-HRMS). Metabolite features (m/z), whose levels significantly differed among the germplasm inbred lines, were identified by ANOVA corrected for FDR and subjected to functional pathway analysis. A number of health-benefiting metabolites linked to dietary starch, antioxidants, vitamins, and lipid metabolism-related compounds were identified. Metabolic genome-wide association analysis (mGWAS) performed using the 396 m/z as phenotypic traits and the 76 K SNP as genotypic variants identified a total of 897 SNPs associated with health benefiting nutritional metabolite at the -log p-value ≤ 4.0. From these associations, 738 probable candidate genes were predicted to have an important role in starch, antioxidants, vitamins, and lipid metabolism. The mGWAS analysis focused on genes involved in starch branching (α-amylase, β-amylase), vitamin-K reductase, UDP-glucuronosyl, and UDP-glucosyl transferase (UGTs), L-ascorbate oxidase, and isoflavone 2′-monooxygenase genes, which are known to be linked to increases in human health benefiting metabolites. We demonstrate how metabolomic, genomic, and statistical approaches can be utilized to pinpoint genetic variations and their functions linked to key nutritional properties in pearl millet, which in turn can be bred into millets and other cereals crops using plant breeding methods

The Challenges and Opportunities Associated with Biofortification of Pearl Millet (Pennisetum glaucum) with Elevated Levels of Grain Iron and Zinc

Deficiencies of essential micronutrients such as iron and zinc are the cause of extensive health problems in developing countries. They adversely affect performance, productivity and are a major hindrance to economic development. Since many people who suffer from micronutrient deficiencies are dependent on staple crops to meet their dietary requirements, the development of crop cultivars with increased levels of micronutrients in their edible parts is becoming increasingly recognized as a sustainable solution. This is largely facilitated by genetics and genomic platforms. The cereal crop pearl millet (Pennisetum glaucum), is an excellent candidate for genetic improvement due to its ability to thrive in dry, semi-arid regions, where farming conditions are often unfavorable. Not only does pearl millet grow in areas where other crops such as maize and wheat do not survive, it contains naturally high levels of micronutrients, proteins and a myriad of other health benefitting characteristics. This review discusses the current status of iron and zinc deficiencies and reasons why interventions such as fortification, supplementation, and soil management are neither practicable nor affordable in poverty stricken areas. We argue that the most cost effective, sustainable intervention strategy is to biofortify pearl millet with enhanced levels of bioavailable iron and zinc. We discuss how naturally occurring genetic variations present in germplasm collections can be incorporated into elite, micronutrient rich varieties and what platforms are available to drive this research. We also consider the logistics of transgenic methods that could facilitate the improvement of the pearl millet gene pool

Genotype-by-Environment Interaction Analysis of Metabolites in Pearl Millet Genotypes with High Concentrations of Slowly Digestible and Resistant Starch in Their Grains

Genotype × environment interactions (GEIs) should play an important role in the selection of suitable germplasm in breeding programmes. We here assessed GEI effects on pearl millet (Pennisetum glaucum L.) genotypes, selected to possess a high concentration of slowly digestible starch (SDS) and resistant starch (RS) in their grains. Entries were grown in a randomized complete block design with three replications at locations in Bawku-Ghana, Sadore-Niger, Bamako-Mali, Konni-Nigeria, and Gampella-Burkina Faso across West Africa. Harvested grains from these locations were metabolomically profiled using flow injection ionization-high-resolution mass spectrometry (FIE-HRMS). A total of 3144 mass features (m/z) (1560 negative ion mode and 1584 positive ion mode) were detected, of which, 475 m/z were linked to metabolites be involved in starch, antioxidant and lipid biosynthesis, and vitamin metabolism. Combined ANOVA revealed that the GEI was significantly evident for 54 health-benefiting metabolites, many associated with sugar, especially galactose, metabolism. Additive main effects and multiplicative interaction (AMMI) analysis examined genotype variation and GEI effects, which, when combined with principal component analysis (PCA), found that m/z 171.14864 (positive ionisation, propenyl heptanoate) accounted for 89% of the GEI variation along PC1. The AMMI-based stability parameter (ASTAB), modified AMMI stability value (MASV), and modified AMMI stability index (MASI) were then applied to identify stable and high-performing genotypes for all the health-benefiting metabolites. Similarly, the best-linear-unbiased-prediction (BLUP)-based stability estimation was also performed using the harmonic mean of genotypic values (HMGV), relative performance of genotypic values (RPGV), and harmonic mean of relative performance of genotypic values (HMRPGV), to identify genotype rankings across multiple environments. The multi-trait stability index (MTSI) was calculated and found that the genotypes G1 (ICMH-177111) and G24 (ICMX-207137) were the most stable and were the best mean performers across 52 health-benefiting metabolic traits. These findings demonstrate the potential of G × E assessments on the delivery of health-benefiting metabolite-rich grains in future varieties and hybrids of pearl millet

Childhood sacrococcygeal teratoma: a clinicopathological study

Background: Sacrococcygeal teratoma (SCT) is a relatively uncommon tumor affecting neonates, infants, and children with a female preponderance. Age is an important predictor of malignancy in SCT. Early antenatal diagnosis influences the management and provides a better outcome. Aim: The present study was carried out to describe in detail various clinicopathological features and outcome of SCT patients; as many reports are available from the West, there is a paucity of literature on this entity from the Eastern region, especially India, which has a unique socioeconomic and demographic background. Materials and methods: The study included 52 patients of SCT operated for 16 years from 2000 to 2015. A retrospective review of various parameters was done from the medical case records available in the Department of Pediatric Surgery (PGIMS, Rohtak, Haryana, India). Result: There were 40 females and 12 males with age ranging from newborn to 13 years. Thirty-three children (63%) presented in the neonatal age group. There were 40 cases of benign (mature), 7 immature and 5 malignant teratomas. Four cases had a recurrence on follow-up. Out of 52 patients, 7 died while the others are doing well on follow-up. Conclusion: A prenatal diagnosis of SCT is essential for reducing morbidity and mortality. Delayed presentation and the presence of malignant changes continue to be poor prognostic factors. Strict follow-up by clinical examination, ultrasound and tumor markers is mandatory to look for any recurrence