Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids

Pearl millet is a non-model grain and fodder crop adapted to extremely hot and dry environments globally. In India, a great deal of public and private sectors’ investment has focused on developing pearl millet single cross hybrids based on the cytoplasmic-genetic male sterility (CMS) system, while in Africa most pearl millet production relies on open pollinated varieties. Pearl millet lines were phenotyped for both the inbred parents and hybrids stage. Many breeding efforts focus on phenotypic selection of inbred parents to generate improved parental lines and hybrids. This study evaluated two genotyping techniques and four genomic selection schemes in pearl millet. Despite the fact that 6· more sequencing data were generated per sample for RAD-seq than for tGBS, tGBS yielded more than 2· as many informative SNPs (defined as those having MAF \u3e 0.05) than RAD-seq. A genomic prediction scheme utilizing only data from hybrids generated prediction accuracies (median) ranging from 0.73-0.74 (1000- grain weight), 0.87-0.89 (days to flowering time), 0.48-0.51 (grain yield) and 0.72-0.73 (plant height). For traits with little to no heterosis, hybrid only and hybrid/inbred prediction schemes performed almost equivalently. For traits with significant mid-parent heterosis, the direct inclusion of phenotypic data from inbred lines significantly (P \u3c 0.05) reduced prediction accuracy when all lines were analyzed together. However, when inbreds and hybrid trait values were both scored relative to the mean trait values for the respective populations, the inclusion of inbred phenotypic datasets moderately improved genomic predictions of the hybrid genomic estimated breeding values. Here we show that modern approaches to genotyping by sequencing can enable genomic selection in pearl millet. While historical pearl millet breeding records include a wealth of phenotypic data from inbred lines, we demonstrate that the naive incorporation of this data into a hybrid breeding program can reduce prediction accuracy, while controlling for the effects of heterosis per se allowed inbred genotype and trait data to improve the accuracy of genomic estimated breeding values for pearl millet hybrids

Performance and Stability of Pearl Millet Varieties for Grain Yield and Micronutrients in Arid and Semi-Arid Regions of India

Pearl millet [Pennisetum glaucum (L.) R. Br.] is grown under both arid and semi-arid conditions in India, where other cereals are hard to grow. Pearl millet cultivars, hybrids, and OPVs (open pollinated varieties) are tested and released by the All India Coordinated Research Project on Pearl Millet (AICRP-PM) across three zones (A1, A, and B) that are classified based on rainfall pattern. Except in locations with extreme weather conditions, hybrids dominate pearl millet growing areas, which can be attributed to hybrid vigor and the active role of the private sector. The importance of OPVs cannot be ruled out, owing to wider adaptation, lower input cost, and timely seed availability to subsidiary farmers cultivating this crop. This study was conducted to scrutinize the presently used test locations for evaluation of pearl millet OPVs across India, identify the best OPVs across locations, and determine the variation in grain Fe and Zn contents across locations in these regions. Six varieties were evaluated across 20 locations in A1 and A (pooled as A) and B zones along with three common checks and additional three zonal adapted checks in the respective zones during the 2019 rainy season. Recorded data on yield and quality traits were analyzed using genotype main effects and genotype × environment interaction biplot method. The genotype × environment (G × E) interaction was found to be highly significant for all the grain yield and agronomic traits and for both micronutrients (iron and zinc). However, genotypic effect (G) was four (productive tillers) to 49 (grain Fe content) times that of G × E interaction effect for various traits across zones that show the flexibility of OPVs. Ananthapuramu is the ideal test site for selecting pearl millet cultivars effectively for adaptation across India, while Ananthapuramu, Perumallapalle, and Gurugram can also be used as initial testing locations. OPVs MP 599 and MP 600 are identified as ideal genotypes, because they showed higher grain and fodder yields and stability compared with other cultivars. Iron and zinc concentration showed highly significant positive correlation (across environment = 0.83; p < 0.01), indicating possibility of simultaneous effective selection for both traits. Three common checks were found to be significantly low yielders than the test entries or zonal checks in individual zones and across India, indicating the potential of genetic improvement through OPVs

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Pearl millet [Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) Morrone], is a staple food for over 90 million poor farmers in arid and semi-arid regions of sub-Saharan Africa and South Asia. We report the ~1.79 Gb genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. Resequencing analysis of 994 (963 inbreds of the highly cross-pollinated cultigen, and 31 wild accessions) provides insights into population structure, genetic diversity, evolution and domestication history. In addition we demonstrated the use of re-sequence data for establishing marker trait associations, genomic selection and prediction of hybrid performance and defining heterotic pools. The genome wide variations and abiotic stress proteome data are useful resources for pearl millet improvement through deploying modern breeding tools for accelerating genetic gains in pearl millet.publishersversionPeer reviewe

Screening of Pearl Millet Genotypes for High Temperature and Drought Tolerance Based on Morpho-Physiological Characters

Aims: Screening of pearl millet genotypes lines for high temperature and drought tolerance. Study Design:&nbsp; Randomized Block Design (RBD) with three replications. Place and Duration of Study: ICAR-AICRP on Pearl Millet, Mandor during summer 2017-18. Methodology: Fifteen genotypes (J-2290, J-2340, J-2479, J-2500, J-2503, J-2507, J-2517, J-2534, JMSB-9904, JMSB-101, JMSB-20064, JMSB-20102, JMSB-20071, JMSB-20082 and JMSB-20091) of pearl millet received from Main Pearl millet Research Station, Junagadh Agricultural University, Jamnagar were evaluated during&nbsp; summer season of 2017-18 at research Farm of ACIRP on pearl millet, Mandor, Agricultural University, Jodhpur under terminal moisture stress&nbsp; and irrigated&nbsp; conditions in two sets of randomized block design with three replications. Grain yield, stover yield, Relative Water Content (RWC), harvest index, threshing percentage and chlorophyll content were recorded. Results: The suitability of the genotypes was judged in terms of grain yield, stover yield, RWC, harvest index, threshing percentage and chlorophyll content. The results showed that due to the terminal stress, the mean performance of all yield attributing characters including grain yield and chlorophyll, RWC and seed setting was reduced. The inbreds J-2479, J-2503 and J-2507 were high yielders due to high seed setting percentage under terminal stress conditions. Conclusion: The lines viz., J-2479, J-2503 and J-2507 can be used for further breeding programme to develop varieties suitable under high temperature and low moisture conditions

Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids

Pearl millet is a non-model grain and fodder crop adapted to extremely hot and dry environments globally. In India, a great deal of public and private sectors’ investment has focused on developing pearl millet single cross hybrids based on the cytoplasmic-genetic male sterility (CMS) system, while in Africa most pearl millet production relies on open pollinated varieties. Pearl millet lines were phenotyped for both the inbred parents and hybrids stage. Many breeding efforts focus on phenotypic selection of inbred parents to generate improved parental lines and hybrids. This study evaluated two genotyping techniques and four genomic selection schemes in pearl millet. Despite the fact that 6· more sequencing data were generated per sample for RAD-seq than for tGBS, tGBS yielded more than 2· as many informative SNPs (defined as those having MAF \u3e 0.05) than RAD-seq. A genomic prediction scheme utilizing only data from hybrids generated prediction accuracies (median) ranging from 0.73-0.74 (1000- grain weight), 0.87-0.89 (days to flowering time), 0.48-0.51 (grain yield) and 0.72-0.73 (plant height). For traits with little to no heterosis, hybrid only and hybrid/inbred prediction schemes performed almost equivalently. For traits with significant mid-parent heterosis, the direct inclusion of phenotypic data from inbred lines significantly (P \u3c 0.05) reduced prediction accuracy when all lines were analyzed together. However, when inbreds and hybrid trait values were both scored relative to the mean trait values for the respective populations, the inclusion of inbred phenotypic datasets moderately improved genomic predictions of the hybrid genomic estimated breeding values. Here we show that modern approaches to genotyping by sequencing can enable genomic selection in pearl millet. While historical pearl millet breeding records include a wealth of phenotypic data from inbred lines, we demonstrate that the naive incorporation of this data into a hybrid breeding program can reduce prediction accuracy, while controlling for the effects of heterosis per se allowed inbred genotype and trait data to improve the accuracy of genomic estimated breeding values for pearl millet hybrids

Levels and causes of maternal mortality in Senegal.

OBJECTIVES: To report the findings of a direct, community-based, assessment of maternal mortality and medical causes of death using verbal autopsy in three unique cohorts in rural Senegal. METHODS: Methods from ongoing demographic surveillance systems. We obtained records of all deaths and births in women of age 15-49 over a period of 14 years in Niakhar, 10 years in Bandafassi and 13 years in Mlomp. Relatives of all women who died were interviewed using a standard questionnaire. Causes of death were assigned by three physicians independently. Maternal deaths were defined according to the ninth and tenth revisions of the International Classification of Diseases. RESULTS: The maternal mortality ratio was similar in Mlomp [436 per 100 000 live births (95% confidence interval 209-802)] and Niakhar [516 per 100 000 (413-636)] but significantly higher in the more remote area of Bandafassi [852 (587-1196)] [relative risk compared with Niakhar 1.6 (1.0-2.4)]. Two-thirds of the maternal deaths were from direct obstetric causes, haemorrhage being the most common. Abortion was rare. CONCLUSIONS: Demographic surveillance systems are useful tools for the measurement of maternal mortality provided special studies are carried out to arrive at the levels and causes of maternal death. The estimates of maternal mortality reported here are lower than those published by the WHO and UNICEF but remain extremely high, particularly in the very remote areas with very limited health infrastructure, where as many as one in 19 women may be expected to die as a consequence of childbirth

I felt so hurt and lonely: Suicidal behavior in South Asian-Surinamese, Turkish, and Moroccan women in the Netherlands

Young immigrant women in the Netherlands demonstrate disproportionate rates of suicidal behavior. This study investigated the origins of suicidal behavior in South Asian-Surinamese, Turkish, and Moroccan immigrant young women in order to identify ethnic- and gender-specific patterns of suicidal behavior. Based on life story interviews of women who had been enrolled in mental health care, we constructed five typical patterns in which social, cultural, and personal factors were interconnected. Suicidal behavior was influenced by the ability and right to act autonomously with regard to strategic life choices, as well as by the questioning of cultural values of self-sacrifice and protection of honor