Charles Tom Hash

Yield, transpiration efficiency, and water-use variations and their interrelationships in the sorghum reference collection

Sorghum is well adapted to water-limited conditions, but the traits responsible for this enhanced adaptation underdroughtconditionsremainunclear.Inthisstudy,yield,transpirationefficiency(TE)andwaterextractionwereassessed in 149 germplasm entries from the sorghum reference set (plus three control cultivars) using a lysimetric system under terminal water stress and fully irrigated conditions outdoors. A 10-fold range for grain yield and harvest index (HI), 2-fold range for TE and a 1.25-fold variation for water extraction were observed under terminal water stress conditions. Transpiration efficiency and water extraction under water stress related poorly to that under fully irrigated conditions, reflectingalargegenotype-by-watertreatmentinteraction.Underdroughtstress,totalwaterextractionvariedby~3Lplant -1 among germplasm. Entries from the Durra race had highest water extraction capacity, whereas Caudatum-Bicolor and Caudatum-Durra intermediate races had poor water extraction. Durra, Caudatum and Caudatum-Guinea races had highest TE,whereastheGuinearacehadthelowest.AlthoughyieldwascloselyrelatedtoHI,atanylevelofHIthereweresubstantial yield differences that remained unexplained, and these residual yield variations were closely related to TE (R 2 =0.60). Similarly,substantialyieldvariationsthatwerestillnotexplainedbyHIorTEwerecloselyrelatedtothetotalwaterextracted underwaterstress(R 2 =0.35).Amultilinearregressionanalysisconfirmedtheseresultsandshowedtheimportanceofwater extractionduringgrain filling.Therefore,nexttoHI,theyielddifferencesunderterminaldroughtinsorghumweredrivenby TE, and then next by water extraction. The large genetic variation for TE and water extraction offer great breeding opportunities and in particular, highlight the Durra race as a critical source of variation.

Toward Sequencing the Sorghum Genome: A U.S. National Science Foundation-Sponsored Workshop Report

Members of the worldwide sorghum (Sorghum spp.) community, including private sector and international scientists as well as community representatives from closely related crops such as sugarcane (Saccharum spp.) and maize (Zea mays), met in St. Louis, Missouri, on November 9, 2004, to lay the groundwork for future advances in sorghum genomics and, in particular, to coordinate plans for sequencing of the sorghum genome. Key developments that made this workshop timely included advances in knowledge of the sorghum genome that provide for the development of a genetically anchored physical map to guide sequence assembly and annotation, the growing role of the sorghum genome as a nucleation point for comparative genomics of diverse tropical grasses including many leading crops, and the need for dramatically increased sorghum production to sustain human populations in many regions where its inherent abiotic stress tolerance makes it an essential staple. This report reviews current knowledge of the sorghum genome, a community-endorsed schema for integrating this knowledge into a finished sequence, and early plans for translating the sequence into sustained advances to benefit a worldwide group of stakeholders.

In silico mapping of important genes and markers available in the public domain for efficient sorghum breeding.

Crop genome sequencing projects generate massive amounts of genomic sequence information, and the utilization of this information in applied crop improvement programs has been augmented by the availability of sophisticated bioinformatics tools. Here, we present the possible direct utilization of sequence data from a sorghum genome sequencing project in applied crop breeding programs. Based on sequence homology, we aligned all publicly available simple sequence repeat markers on a sequence-based physical map for sorghum. Linking this physical map with already existing linkage map(s) provides better options for applied molecular breeding programs. When a new set of markers is made available, the new markers can be first aligned on a sequence-based physical map, and those located near the quantitative trait locus (QTL) can be identified from this map, thereby reducing the number of markers to be tested in order to identify polymorphic flanking markers for the QTL for any given donor × recurrent parent combination. Polymorphic markers that are expected (on the basis of their position on the sequence-based physical map) to be closely linked to the target can be used for foreground selection in marker-assisted breeding. This map facilitates the identification of a set of markers representing the entire genome, which would provide better resolution in diversity analyses and further linkage disequilibrium mapping. Filling the gaps in existing linkage maps and fine mapping can be achieved more efficiently by targeting the specific genomic regions of interest. It also opens up new exciting opportunities for comparative mapping and for the development of new genomic resources in related crops, both of which are lagging behind in the current genomic revolution. This paper also presents a number of examples of potential applications of sequence-based physical map for sorghum.

Population Genetics and Structure of a Global Foxtail Millet Germplasm Collection

Foxtail millet [Setaria italica (L.) P. Beauv.] is one among the most ancient crops of dryland agriculture. It is the second most important crop among millets grown for grains or forage. Foxtail millet germplasm resources provide reservoirs of novel alleles and genes for crop improvement that have remained mostly unexplored. We genotyped a set of 190 foxtail millet germplasm accessions (including 155 accessions of the foxtail millet core collection) using genotyping‐by‐sequencing (GBS) for rapid single nucleotide polymorphisms (SNP) characterization to study population genetics and structure, which enable allele mining through association mapping approaches. After filtering a total 350,000 raw SNPs identified across 190 germplasm accessions for minor allele frequency (MAF), coverage for samples and coverage for sites, we retained 181 accessions with 17,714 high‐quality SNPs with ≥5% MAF. Genetic structure analyses revealed that foxtail millet germplasm accessions are structured along both on the basis of races and geographic origin, and the maximum proportion of variation was due to among individuals within populations. Accessions of race indica were less diverse and are highly differentiated from those of maxima and moharia. Genome‐wide linkage disequilibrium (LD) analysis showed on an average LD extends up to ∼150 kbp and varied with individual chromosomes. The utility of the data for performing genome‐wide association studies (GWASs) was tested with plant pigmentation and days to flowering and identified significant marker–trait associations. This SNP data provides a foundation for exploration of foxtail millet diversity and for mining novel alleles and mapping genes for economically important traits.

Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits

A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with ‘stay green’ phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet drought tolerance.

A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae).

PREMISE OF THE STUDY Discrepancies in terms of genotyping data are frequently observed when comparing simple sequence repeat (SSR) data sets across genotyping technologies and laboratories. This technical concern introduces biases that hamper any synthetic studies or comparison of genetic diversity between collections. To prevent this for Sorghum bicolor, we developed a control kit of 48 SSR markers. METHODS AND RESULTS One hundred seventeen markers were selected along the genome to provide coverage across the length of all 10 sorghum linkage groups. They were tested for polymorphism and reproducibility across two laboratories (Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement [CIRAD], France, and International Crops Research Institute for the Semi-Arid Tropics [ICRISAT], India) using two commonly used genotyping technologies (polyacrylamide gel-based technology with LI-COR sequencing machines and capillary systems with ABI sequencing apparatus) with DNA samples from a diverse set of 48 S. bicolor accessions. CONCLUSIONS A kit for diversity analysis (http://sat.cirad.fr/sat/sorghum_SSR_kit/) was developed. It contains information on 48 technically robust sorghum microsatellite markers and 10 DNA controls. It can further be used to calibrate sorghum SSR genotyping data acquired with different technologies and compare those to genetic diversity references.

First products of DNA marker-assisted selection in sorghum released for cultivation by farmers in sub-saharan Africa

Striga hermonthica (Del.) Benth. is the major biotic constraint to sorghum production. Its control is difficult and can only be achieved through integrated management strategies that depend mainly on host plant resistance and enhanced soil fertility. However, breeding for resistance is hampered by the complexity of host parasite interactions and lack of reliable screening methods. The invention of molecular markers has enhanced the effectiveness of breeding for resistance. Five genomic regions (QTLs) with linked markers associated with Striga resistance were mapped in sorghum variety N13 by [10]. In this study, to increase the efficiency of marker-assisted selection (MAS), 27 EST-SSR markers in close association with Striga resistance QTLs were also identified and mapped. Populations of backcross (BC3S4) derived from N13 (Striga resistant) X three farmer preferred sorghum cultivars: Tabat, Wad Ahmed and AG-8 (Striga susceptible) were generated. Thirty-one lines (BC3S4) with confirmed Striga field resistance were genotyped with foreground and background selection makers. Twenty resistant lines, with two or more major QTLs were selected for regional evaluation. Of these 10 lines were selected and advanced for multi-location testing, together with Wad Ahmed, Tabat, AG-8, N13, SRN39 and IS9830 as checks. Standard variety trials were conducted in Striga sick plots over three seasons (2009-2011) in Sudan, Gezira Research Station, Damazine, Sinnar, and Gedarif. Results revealed that four lines (T1BC3S4, AG6BC3S4, AG2BC3S4 and W2BC3S4) were Striga resistant and agronomically superior with yields ranging from 180% to 298% higher relative to their recurrent parents. This Striga resistance coupled with superior attributes of the recurrent parent (including very high yield potentials, high grain quality and drought tolerance) will provide adaptation and stability across a wide range of environments. These are the first products of DNA markerassisted selection (MAS) in sorghum released for cultivation by farmers in sub-Saharan Africa.

Mapping Quantitative Trait Loci Controlling High Iron and Zinc Content in Self and Open Pollinated Grains of Pearl Millet [Pennisetum glaucum (L.) R. Br.]

Pearl millet is a multipurpose grain/fodder crop of the semi-arid tropics, feeding many of the world’s poorest and most undernourished people. Genetic variation among adapted pearl millet inbreds and hybrids suggests it will be possible to improve grain micronutrient concentrations by selective breeding. Using 305 loci, a linkage map was constructed to map QTLs for grain iron [Fe] and zinc [Zn] using replicated samples of 106 pearl millet RILs (F6) derived from ICMB 841-P3 × 863B-P2. The grains of the RIL population were evaluated for Fe and Zn content using atomic absorption spectrophotometer. Grain mineral concentrations ranged from 28.4 to 124.0 ppm for Fe and 28.7 to 119.8 ppm for Zn. Similarly, grain Fe and Zn in open pollinated seeds ranged between 22.4–77.4 and 21.9–73.7 ppm, respectively. Mapping with 305 (96 SSRs; 208 DArT) markers detected seven linkage groups covering 1749 cM (Haldane) with an average intermarker distance of 5.73 cM. On the basis of two environment phenotypic data, two co-localized QTLs for Fe and Zn content on linkage group (LG) 3 were identified by composite interval mapping (CIM). Fe QTL explained 19% phenotypic variation, whereas the Zn QTL explained 36% phenotypic variation. Likewise for open pollinated seeds, the QTL analysis led to the identification of two QTLs for grain Fe content on LG3 and 5, and two QTLs for grain Zn content on LG3 and 7. The total phenotypic variance for Fe and Zn QTLs in open pollinated seeds was 16 and 42%, respectively. Analysis of QTL × QTL and QTL × QTL × environment interactions indicated no major epistasis.

SSR allelic diversity in relation to morphological traits and resistance to grain mould in sorghum

Allelic variation at 46 simple sequence repeat (SSR) marker loci well distributed across the sorghum genome was used to assess genetic diversity among 92 sorghum lines, 74 resistant and 18 susceptible to grain mould. Of the 46 SSR markers, 44 were polymorphic, with the number of alleles ranging from 2 to 20 with an average of 7.55 alleles per locus. Genetic diversity among the sorghum lines was high as indicated by polymorphic information content (PIC) and gene diversity values. PIC values of polymorphic SSR markers ranged from 0.16 to 0.90, with an average of 0.54. Gene diversity among the sorghum lines varied from 0.16 to 0.91, with an average score of 0.58 per SSR marker. AMOVA indicated that 12% of the total variation observed among the sorghum lines was accounted for between grain mould resistant and susceptible types. Diversity based on six morphological traits and grain mould scores indicated major roles of panicle type and glumes coverage, followed by grain colour, in clustering of the lines. Seven grain mould resistant/ susceptible pairs with dissimilarity indices >0.50, but with similar flowering time, plant height, and panicle type/ inflorescence within each pair, were selected for use in developing recombinant inbred line mapping populations to identify genomic regions (and quantitative trait loci) associated with sorghum grain mould resistance.

Overcoming Phosphorus Deficiency in West African Pearl Millet and Sorghum Production Systems: Promising Options for Crop Improvement.

West Africa (WA) is among the most food insecure regions. Rapid human population growth and stagnating crop yields greatly contribute to this fact. Poor soil fertility, especially low plant available phosphorus (P) is constraining food production in the region. P-fertilizer use in WA is among the lowest in the world due to inaccessibility and high prices, often unaffordable to resource-poor subsistence farmers. This article provides an overview of soil P-deficiency in WA and opportunities to overcome it by exploiting sorghum and pearl millet genetic diversity. The topic is examined from the perspectives of plant breeding, soil science, plant physiology, plant nutrition, and agronomy, thereby referring to recent results obtained in a joint interdisciplinary research project, and reported literature. Specific objectives are to summarize: (1) The global problem of P scarcity and how it will affect WA farmers; (2) Soil P dynamics in WA soils; (3) Plant responses to P deficiency; (4) Opportunities to breed for improved crop adaptation to P-limited conditions; (5) Challenges and trade-offs for improving sorghum and pearl millet adaptation to low-P conditions in WA; and (6) Systems approaches to address soil P-deficiency in WA. Sorghum and pearl millet in WA exhibit highly significant genetic variation for P-uptake efficiency, P-utilization efficiency, and grain yield under P-limited conditions indicating the possibility of breeding P-efficient varieties. Direct selection under P-limited conditions was more efficient than indirect selection under high-P conditions. Combining P-uptake and P-utilization efficiency is recommendable for WA to avoid further soil mining. Genomic regions responsible for P-uptake, P-utilization efficiency, and grain yield under low-P have been identified in WA sorghum and pearl millet, and marker-assisted selection could be possible once these genomic regions are validated. Developing P-efficient genotypes may not, however, be a sustainable solution in itself in the long-term without replenishing the P removed from the system in harvested produce. We therefore propose the use of integrated soil fertility management and systems-oriented management such as enhanced crop-tree-livestock integration in combination with P-use-efficiency-improved varieties. Recycling P from animal bones, human excreta and urine are also possible approaches toward a partially closed and efficient P cycle in WA.