Sorghum

SSR-based assessment of genetic diversity in sorghum has been a major activity in Subprogram 1 of the Generation Challenge Program (GCP) over the past three years, and ICRISAT contributed to this with partners from CIRAD (France) and CAAS (China). Our goal was to genotype a composite collection of
3,000 accessions at 50 SSR loci that were well-distributed across nearly the full length of all 10 sorghum linkage groups. We have succeeded in genotyping some 3,400 accessions across 39 loci, and diversity analysis of this data set has provided substantial information on population structure of sorghum germplasm globally and permitted selection of a highly informative reference set of 300 accessions for detailed study in future. Similar diversity studies are underway targeting sorghum germplasm from several NARS partners in Africa, with support from BMZ, USAID, the GCP, and as part of the African Biofortified Sorghum project. At Patancheru, we are now initiating a similar diversity study of elite sorghum hybrid parental lines, with the intention of assessing opportunities to identify combining ability groups.

Collaborative efforts of CIRAD (France) with Diversity Arrays Technology Pty Ltd (DArT, Australia) have resulted in DArT arrays for sorghum. DArT markers detected by these arrays have been demonstrated to possess the potential for undertaking the genome-wide diversity studies in sorghum at lower operational cost and in less time than would be needed for SSRs. DArT facilities are being established at ICRISAT as a part of the Centre of Excellence in Genomics (CEG), which will enhance our diversity assessment and utilization program.

In SSA, SSR markers are being used at the ILRI/BecA laboratory to study genetic relationships and diversity in two key ICRISAT mandate crops-sorghum and pearl millet. Through a Rockefeller Foundation/GCP/BecA funded project, a subset of the molecular markers developed under the GCP initiative are being used to study sorghum genetic diversity in 1,600 accessions of germplasm held by eight NARS in East and Southern Africa, including Burundi, Ethiopia, Eritrea, Kenya, Rwanda, Sudan and Tanzania. In West Africa, molecular markers have been used extensively in the past to study agrobiodiversity in Mali, diversity of guinea-race sorghum landraces and the evolution of sorghum and pearl millet diversity in Niger by CIRAD in collaboration with ICRISAT. They have also been used to understand the evolutionary relationships between sorghum and pearl millet and their wild relatives. Molecular markers are being used in heterotic grouping of West and Central African sorghum and pearl millet landraces.

Pearl millet

ICRISAT is expanding SSR-based studies of genetic diversity in pearl millet in a GCP-sponsored project on SSR genotyping at 20 loci of up to 1,000 accessions. This study will provide allele frequency estimation in heterogenous landrace germplasm accessions and improved open-pollinated varieties, as well as a range of genetic stocks and elite inbred lines. In addition, we are involved with national program partners in Africa in assessing diversity within and between important improved and landrace cultivars with support from BMZ and the GCP, and have initiated a project at Patancheru to characterize elite B- and R-lines on the basis of morphological and SSR-based diversity.

In order to exploit the potential of SNP markers for diversity assessment, a pilot study involving screening of 24 inbred lines with hundreds of SSR, CISP (conserved intron spanning primers), and SSCP-based SNP assays demonstrated the high polymorphism information content of SNP assays in pearl millet. Thus, now it is possible to undertake SNP assays in pearl millet. although the cost per data point is high compared to SSRs.

Chickpea

Working together in the GCP, ICRISAT and ICARDA have completed genotyping of a composite collection of 3,000 accessions at 50 SSR loci distributed across the chickpea genome. The information obtained from this study has improved our understanding of the structure of genetic variation in chickpea. We have selected a reference set of 300 accessions consisting of a chickpea mini-core (211 accessions) plus 89 other accessions capturing the maximum diversity in the composite collection. The reference collection is being used for extensive phenotyping for different traits and for genotyping using a large number of markers for association studies. This reference collection is also being used for screening with 15 candidate drought responsive genes for exploring the potential of candidate gene sequence-based association studies for drought tolerance.

Groundnut

We have completed a major SSR-based diversity assessment in groundnut, with support from the Generation Challenge Program, which has targeted genotyping of 1,000 accessions at 20 SSR loci, in collaboration with EMBRAPA, Brazil. Data analysis is in progress and results will be used to select a reference set of 300 most diverse accessions.

Pigeonpea

A genotyping project aimed at understanding the heterogeneity, population structure as well as relationships among 1,000 pigeonpea lines at 20 SSR loci has been completed and analysis of the dataset is underway at ICRISAT, with support from the GCP.

Finger millet

A genotyping project aimed at understanding the population structure among 1,000 finger millet lines at 20 recently mapped SSR loci has been completed and analysis of the dataset is underway at ICRISAT, with support from the GCP.

Other minor millets

A genotyping project to assess population structure and relationships between 500 foxtail millet accessions is underway at ICRISAT with support from the GCP. Since SSR markers have not been isolated in foxtail millet, we have made use of primers for finger millet and pearl millet SSR markers. For example, after screening a set of 93 pearl millet and 31 finger millet SSR primer pairs on two foxtail genotypes (ISC 31, ISC 746), 39 SSR markers (26 pearl millet and 13 finger millet) that yielded amplicons from the foxtail millet genotypes were identified. Subsequently, a set of 20 polymorphic SSR markers was identified after screening these 39 SSR markers on eight diverse foxtail millet genotypes. Genotyping of the foxtail millet composite collection with the selected SSR markers is currently underway.

Gene flow surveys

Gene flow is a major evolutionary force that largely contributes to the in situ dynamics of genetic diversity. It refers to the movement of genes both within a population (gene dispersal) and among populations (migration). In the semi-arid regions of sub-Saharan Africa, farmers still mainly grow traditional varieties of food crops, and select the seeds for replanting the next season. These traditional varieties generally exhibit a significant diversity within and among seed lots.

ICRISAT has been leading several projects in West and East Africa on gene flow using both direct experimental approaches and indirect genetic marker based inferences. The objectives of these studies are to better understand the in situ evolution of crop diversity in relation to biological, environmental and anthropogenic factors. This will provide critical information for the: i) improvement of the efficiency of in situ conservation programs, ii) strengthening of the complementarity between traditional and commercial seed systems, and iii) science-based decisions regarding the environmental risk assessment of genetically engineered crops.

In sub-Saharan Africa, sorghum has been identified as a model crop for gene flow surveys due to its mixed mating system with a preferential selfing but a significant outcrossing rate (generally around 20%), the maintenance of an outstanding varietal diversity by farmers, the predominance of traditional farmers' practices in most sorghum growing areas, and the presence of wild and weedy relatives close to farmers' fields.

i) Pollen mediated crop-to-crop gene flow

In collaboration with the University of Hohenheim, on station experiments have been conducted using male sterile lines as pollen traps to estimate the shape and parameters of sorghum pollen dispersal functions. This approach is being extended to real farming conditions in Kenya where several stronger and unevenly distributed pollen sources determine the spatial patterns of pollen clouds in the agro-ecosystems. Simultaneously, SSR markers are being used to infer gene flow among varieties on a wider temporal scale.

Indirect and direct estimations of gene flow will provide insights on the impact of farmers' practices on the structure of sorghum genetic diversity and help predict the dissemination of genes (eg, Striga resistance genes, transgenes) among varieties and farmers' fields.

ii) Seed mediated crop-to-crop gene flow

In sub-Saharan Africa, farmers either exchange seeds within a socially structured network or obtain them from external seed sources (markets, NGOs, seed emergency programs). The structure of diversity is also the result of seed exchange practices. SSR markers are being used on sorghum and pearl millet in Kenya to assess the seed mediated gene flow in socially and environmentally structured regions. Molecular markers are useful tools to measure the dissemination of local and modern varieties on-farm and help identify agro-ecological, agronomic and socio-economic niches for improved varieties. Gene flow activities can therefore be the place of innovative collaborations between geneticists, breeders, social scientists and GIS/agro-ecologists in the framework of the IGNRM concept.

iii) Gene flow between crops and their wild relatives

Gene transfers between a crop and its wild relatives are special cases of gene flow. In 6 SSA countries (Mali, Kenya, South Africa, Burkina Faso, Nigeria, Egypt), ICRISAT is conducting surveys to measure crop-to-wild gene flow in the perspective of environmental risk assessment of GM crops. These surveys assess the different factors that can favor or prevent gene flow, eg, like biological compatibility between wild and cultivated sorghums, phenological overlaps, pollen dispersal and spatial connectivity of wild/weedy and cultivated sorghum habitats, and crop-wild hybrid fitness.

For further information, contact: Dave Hoisington, Rajeev Varshney (legume diversity), Tom Hash (cereal diversity), Dan Kiambi (Africa diversity), Fabrice Sagnard (gene flow)