Mining crop genomic variation can facilitate the genetic research of complex traits and molecular breeding. In sorghum [ L. (Moench)], several large-scale single nucleotide polymorphism (SNP) datasets have been generated using genotyping-by-sequencing of KI reduced representation libraries. However, data reuse has been impeded by differences in reference genome coordinates among datasets. To facilitate reuse of these data, we constructed and characterized an integrated 459,304-SNP dataset for 10,323 sorghum genotypes on the version 3.1 reference genome. The SNP distribution showed high enrichment in subtelomeric chromosome arms and in genic regions (48% of SNPs) and was highly correlated ( = 0.82) to the distribution of KI restriction sites. The genetic structure reflected population differences by botanical race, as well as familial structure among recombinant inbred lines (RILs). Faster linkage disequilibrium decay was observed in the diversity panel than in the RILs, as expected, given the greater opportunity for recombination in diverse populations. To validate the quality and utility of the integrated SNP dataset, we used genome-wide association studies (GWAS) of genebank phenotype data, precisely mapping several known genes (e.g and ) and identifying novel associations for other traits. We further validated the dataset with GWAS of new and published plant height and flowering time data in a nested association mapping population, precisely mapping known genes and identifying epistatic interactions underlying both traits. These findings validate this integrated SNP dataset as a useful genomics resource for sorghum genetics and breeding.

An Integrated Genotyping-by-Sequencing Polymorphism Map for Over 10,000 Sorghum Genotypes.

Cowpea is one of the major food crops contributing to food security and poverty alleviation in Benin. In order to identify performing varieties that could meet producers’ and consumers’ needs, and to collect ethnobotanical data that will help preserving varietal diversity, twenty eight (28) villages randomly selected in southern Benin were surveyed using participatory research appraisal. The survey revealed the existence of a non-negligible diversity of cowpea varieties in the study zone. Subject to synonymy, 92 farmer-named varieties were identified and the Shannon–Weaver diversity index (H) was estimated at 3.31. The number of varieties recorded varied from 7 to 16 per village (9 on average) and from 1 to 6 per household (3 on average). The distribution and extent analysis revealed that many varieties were being disappeared leading to a production mainly concentrated on a small number (4 on average per village) of varieties cultivated by many households and on large areas. The average rate of diversity loss was 28%. A participatory agronomic and culinary evaluation of the varieties carried out with 12 parameters yielded 3 to 76 varieties per evaluation traits. The less provided evaluation traits were tolerance to field insects, diseases, weeds and storage insects with only 3, 5, 6 and 10 varieties respectively. Based on the agronomic and culinary variables used, the 92 varieties recorded were grouped into 54 different units consisted of 1 to 11 varieties. Farmers’ preference criteria were identified and prioritized for use by eventual breeding and variety exchange programmes. Identified varieties were collected and their characterization was recommended.

Diversity and agronomic performances of the cowpea (Vigna unguiculata Walp.) landraces in Southern Benin

Sorghum is one of the most important cereal crops worldwide after wheat, rice, maize and barley. Examining the present socio-economic conditions of sorghum-producing farmers in different agro-ecologies in Ethiopia is of importance for the design of improvement strategies. The objectives of this study were to evaluate the sorghum production system and patterns, major production constraints and related coping strategies in north-eastern Ethiopia. Twelve sorghum-growing villages in the North Welo, South Welo and Waghemra districts were surveyed. Descriptive statistics and a generalised additive model were used for data analysis. Constraints affecting the productivity of sorghum include moisture stress, insect pests, striga, farmland shortage, poor soil fertility, diseases, and low-yielding local cultivars. Among the constraints, drought at the grain-filling stage was identified as the most important production problem in the target region. The productivity of sorghum was also hindered by the use of local drought-tolerant but low-yielding landraces, because farmers had been forced to abandon high-yielding and late-maturing landrace cultivars because of the frequent occurrence of drought. To enhance sorghum productivity, farmers’ knowledge and practices, and production constraints need to be integrated from the initial stages of breeding and technology development.Keywords: generalised additive model, moisture stress, participatory rural appraisal, production constraint, sorghum

https://www.tandfonline.com/doi/pdf/10.1080/02571862.2016.1143043

Sorghum production systems and constraints, and coping strategies under drought-prone agro-ecologies of Ethiopia

This chapter surveys the conceptual basis of indicators of genetic diversity, genetic erosion, and genetic vulnerability. These are summary measures of genetic diversity in cultivated plants and their wild relatives that guide decisions, monitor progress, and warn of emerging issues of genetic resources for resilient agricultural production. Such indicators measure the genetic diversity currently present in agricultural populations on farm and held in germplasm collections, and aim to detect genetic erosion, or serious loss of diversity in time, and to warn of vulnerability due to adverse deployment of genetic diversity in space. While diversity itself encompasses many concepts, richness diversity—the number of different kinds of individuals regardless of their frequencies—is the most important theme, followed by evenness diversity—how similar the frequencies of the different variants are. Many variables are plausible as indicators of diversity. The more practical are based on number of individuals or area occupied in situ and on the number of accessions and the number of genebanks ex situ. Genetic erosion is measurable as the proportion of richness of genetic diversity no longer existing in current populations, when compared with the crop a decade previously or predicted to be lost in the next decade without remedial action. Genetic vulnerability is inversely related to richness diversity that is present locally, particularly if it is known to possess adaptation to exotic or new mutant pathotypes or insect strains or environments. Census information forms the primary data. For cultivated species, these data are based on the farmer’s unit of diversity management, most often their named varieties, their number, relative frequencies and divergence over various units of spatial and temporal scale. For wild species, the analogous units of diversity are the lowest recognized (e.g. subspecies, morphological types, ecotypes). Census data should be supplemented and validated using more direct assays at the DNA level with molecular techniques in carefully constructed samples.

Indicators of Genetic Diversity, Genetic Erosion, and Genetic Vulnerability for Plant Genetic Resources

The dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. However, few surveys have been conducted in centres of diversity. Sub-Saharan Africa is the centre of origin of sorghum. Most Sahel countries have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic erosion. Sorghum is the second staple cereal in Niger, a centre of diversity for this crop. Niger was submitted to recurrent drought period and to major social changes during these last decades. We report here on a spatio-temporal analysis of sorghum genetic diversity, conducted in 71 villages covering the rainfall gradient and range of agro-ecological conditions in Niger's agricultural areas. We used 28 microsatellite markers and applied spatial and genetic clustering methods to investigate change in genetic diversity over a 26-year period (1976-2003). Global genetic differentiation between the two collections was very low (F (st) = 0.0025). Most of the spatial clusters presented no major differentiation, as measured by F (st), and showed stability or an increase in allelic richness, except for two of them located in eastern Niger. The genetic clusters identified by Bayesian analysis did not show a major change between the two collections in the distribution of accessions between them or in their spatial location. These results suggest that farmers' management has globally preserved sorghum genetic diversity in Niger.

/pdf/spatio-temporal-dynamics-of-genetic-diversity-in-sorghum-dqyvppnrzj.pdf

Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger

Temporal and spatial changes of sorghum landrace diversity and related factors in five farming communities in north Shewa and south Welo, between 1992/1993 and 2000/2001, were studied in order to ascertain the stability of a range of factors that support the maintenance of the crop genetic diversity. The same farmers were interviewed and the same sorghum fields were surveyed both times. Over the 8-year period: the total area planted to sorghum decreased drastically in all five farming communities and a large percentage of the farmers in the communities (Hayk, 69%; Borkena, 68%; Epheson,  51%; Merewa Adere, 72%; and Bati, 54%) decreased the field size planted to sorghum, because of population growth, land redistribution policy, seasonal changes, and stagger cropping followed by interspecies crop displacement; landrace richness increased significantly in Merewa and Borkena, but decreased significantly in Bati, Epheson and Hayk; and farmers’ selection criteria, the reasons for growing specific landraces, increased significantly (10 in 1992/1993 vs. 22 in 2000/2001). Significant differences in field size distribution occur among the five farming communities. In 2000/2001, 22 “generalist” landraces (grown widely across three or more communities), and 46 “specialist” landraces (niche specific, restricted to certain microhabitats in one or two communities) were found. Landrace gains and losses from the farms surveyed in individual communities over the period are demonstrated.

Changes of Sorghum bicolor landrace diversity and farmers’ selection criteria over space and time, Ethiopia

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Changes of Sorghum bicolor landrace diversity and farmers’ selection criteria over space and time, Ethiopia