Eva Weltzien

Analysis of >1000 single nucleotide polymorphisms in geographically matched samples of landrace and wild barley indicates secondary contact and chromosome‐level differences in diversity around domestication genes

Barley is a model species for the investigation of the evolution, adaptation and spread of the worlds important crops. In this article, we describe the first application of an oligonucleotide pool assay single nucleotide polymorphism (SNP) platform to assess the evolution of barley in a portion of the Fertile Crescent, a key region in the development of farming. A large collection of >1000 genetically mapped, genome-wide SNPs was assayed in geographically matched landrace and wild barley accessions (N=448) from Jordan and Syria. Landrace and wild barley categories were clearly genetically differentiated, but a limited degree of secondary contact was evident. Significant chromosome-level differences in diversity between barley types were observed around genes known to be involved in the evolution of cultivars. The region of Jordan and southern Syria, compared with the north of Syria, was supported by SNP data as a more likely domestication origin. Our data provide evidence for hybridization as a possible mechanism for the continued adaptation of landrace barley under cultivation, indicate regions of the genome that may be subject to selection processes and suggest limited origins for the development of the cultivated crop.

A yield architecture framework to explain adaptation of pearl millet to environmental stress

Functional knowledge of the physiological basis of crop adaptation to stress is a prerequisite for exploiting specific adaptation to stress environments in breeding programs. This paper presents an analysis of yield components for pearl millet, to explain the specific adaptation of local landraces to stress environments in Rajasthan, India. Six genotypes, ranging from high-tillering traditional landraces to low-tillering open-pollinated modern cultivars, were grown in 20 experiments, covering a range of nonstress and drought stress patterns. In each experiment, yield components (particle number, grain number, 100 grain mass) were measured separately for main shoots, basal tillers, and nodal tillers. Under optimum conditions, landraces had a significantly lower grain yield than the cultivars, but no significant differences were observed at yield levels around 1 ton ha(-1). This genotype x environment interaction for grain yield was due to a difference in yield strategy, where landraces aimed at minimising the risk of a crop failure under stress conditions, and modem cultivars aimed at maximising yield potential under optimum conditions. A key aspect of the adaptation of landraces was the small size of the main shoot panicle, as it minimised (1) the loss of productive tillers during stem elongation; (2) the delay in anthesis if mid-season drought occurs; and (3) the reduction in panicle productivity of the basal tillers under stress. In addition, a low investment in structural panicle weight, relative to vegetative crop growth rate, promoted the production of nodal tillers, providing a mechanism to compensate for reduced basal tiller productivity if stress occurred around anthesis. A low maximum 100 grain mass also ensured individual grain mass was little affected by environmental conditions. The strategy of the high-tillering landraces carries a yield penalty under optimum conditions, but is expected to minimise the risk of a crop failure, particularly if mid-season drought stress occurs. The yield architecture of low-tillering varieties, by contrast, will be suited to end-of-season drought stress, provided anthesis is early. Application of the above adaptation mechanisms into a breeding program could enable the identification of plant types that match the prevalent stress patterns in the target environments

Effects of farmers' seed management on performance and adaptation of pearl millet in Rajasthan, India

Pearl millet (Pennisetum glaucum [L.]R.Br.) is the staple food and fodder crop of farmers in the semi-arid areas of north-west India. The majority of farmer sin western Rajasthan depend on their own seed production and employ different seed production strategies that involve different levels of modern-variety introgression into landraces as well as different selection methods. This study quantifies the effects of three seed management strategies on environmental adaptation and trait performance. Forty-eight entries representing farmers’ grain stocks — pure landraces or landraces with introgressed germ plasm from modern varieties — as well as 33 modern varieties, multiplied by breeders or farmers, were evaluated in field trials at three different locations over two years under varying drought-stress conditions. Results indicate that the plant characteristics employed by farmers in describing adaptive value and productivity is an effective approach in discriminating the type of millet adapted to stress and non-stress conditions. It was also found that introgression of modern varieties(MVs) leads to populations with a broader adaptation ability in comparison to pure landraces or MVs alone – but only if MV introgression is practised regularly and is combined with mass panicle selection. Under high-rainfall conditions, farmer grain stocks with MV introgression show similar productivity levels as modern varieties. Under lessening rainfall, pure landraces show, in tendency, higher grain yields. In conclusion, farmers’ seed management could form an integral part of participatory breeding programs.

Two in one sweep: aluminum tolerance and grain yield in P-limited soils are associated to the same genomic region in West African Sorghum

BackgroundSorghum (Sorghum bicolor L. Moench) productivity is severely impeded by low phosphorus (P) and aluminum (Al) toxic soils in sub-Saharan Africa and especially West Africa (WA). Improving productivity of this staple crop under these harsh conditions is crucial to improve food security and farmer’s incomes in WA.ResultsThis is the first study to examine the genetics underlying sorghum adaptation to phosphorus limitation in a wide range of WA growing conditions. A set of 187 diverse sorghum genotypes were grown in 29 –P and + P field experiments from 2006-2012 in three WA countries. Sorghum grain yield performance under –P and + P conditions was highly correlated (r = 0.85***). Significant genotype-by-phosphorus interaction was detected but with small magnitude compared to the genotype variance component. We observed high genetic diversity within our panel, with rapid linkage disequilibrium decay, confirming recent sequence based studies in sorghum. Using genome wide association mapping based on 220 934 SNPs we identified one genomic region on chromosome 3 that was highly associated to grain yield production. A major Al-tolerance gene in sorghum, SbMATE, was collocated in this region and SbMATE specific SNPs showed very high associations to grain yield production, especially under –P conditions, explaining up to 16% of the genotypic variance.ConclusionThe results suggest that SbMATE has a possible pleiotropic role in providing tolerance to two of the most serious abiotic stresses for sorghum in WA, Al toxicity and P deficiency. The identified SNPs can help accelerate breeding for increased sorghum productivity under unfavorable soil conditions and contribute to assuring food security in WA.

Phosphorus uptake and use efficiency of diverse West and Central African sorghum genotypes under field conditions in Mali

AimsSorghum [Sorghum bicolor (L.) Moench], a staple crop in West and Central Africa (WCA), is mostly cultivated on soils with low phosphorus (P) availability and thus adaptation to those conditions is vital for food security. Assessment of genotypic variation of WCA sorghum for P uptake and P use efficiency is undertaken to understand the diversity available and opportunities for its use.MethodWe assessed mature plant yield, P uptake and P use efficiency traits of 70 diverse WCA sorghum genotypes under –P (no P fertilization) and + P field conditions in Mali in 2010, to discover differences among all genotypes tested and between and within specific genotype groups.ResultsLarge significant genotypic variation for P uptake and P use efficiency traits were observed for all genotypes among and within landrace and researcher bred pools under –P conditions. P uptake traits had a larger genotypic variation than P use efficiency traits. Landrace genotypes showed generally higher P uptake and grain P concentration while formally bred genotypes exhibited a higher P use efficiency. Photoperiod sensitivity was related to higher P uptake.ConclusionGenotypic selection for P uptake and P use efficiency traits to improve adaptation to low P soils is possible in sorghum. Use and further study of WCA sorghums for adaptation to low P availability is appropriate as this germplasm shows large variation for P uptake and use efficiency and higher levels of P use efficiency than other important cereals.

Association analysis of photoperiodic flowering time genes in west and central African sorghum [Sorghum bicolor (L.) Moench].

BackgroundPhotoperiod-sensitive flowering is a key adaptive trait for sorghum (Sorghum bicolor) in West and Central Africa. In this study we performed an association analysis to investigate the effect of polymorphisms within the genes putatively related to variation in flowering time on photoperiod-sensitive flowering in sorghum. For this purpose a genetically characterized panel of 219 sorghum accessions from West and Central Africa was evaluated for their photoperiod response index (PRI) based on two sowing dates under field conditions.ResultsSorghum accessions used in our study were genotyped for single nucleotide polymorphisms (SNPs) in six genes putatively involved in the photoperiodic control of flowering time. Applying a mixed model approach and previously-determined population structure parameters to these candidate genes, we found significant associations between several SNPs with PRI for the genes CRYPTOCHROME 1 (CRY1-b1) and GIGANTEA (GI).ConclusionsThe negative values of Tajimas D, found for the genes of our study, suggested that purifying selection has acted on genes involved in photoperiodic control of flowering time in sorghum. The SNP markers of our study that showed significant associations with PRI can be used to create functional markers to serve as important tools for marker-assisted selection of photoperiod-sensitive cultivars in sorghum.

Population structure in sorghum accessions from West Africa differing in race and maturity class

Accounting for population structure to minimize spurious associations in association analyses is of crucial importance. With sorghum genomic sequence information being available, there is a growing interest in performing such association studies for a number of important agronomic traits using a candidate gene approach. The aims of our study were to conduct a systematic survey of molecular genetic diversity and analyze the population structure in cultivated sorghum [Sorghum bicolor (L.) Moench] accessions from West Africa. Our analysis included 219 West African cultivated sorghum accessions with differing maturity intended for a marker-trait association study. A total of 27 SSRs were used, which resulted in detection of 513 alleles. Genetic diversity estimates for the accessions were found to be high. The accessions were divided into two subgroups using a model-based approach. Our findings partly agree with previous studies in that the guinea race accessions could be distinguished clearly from other accessions included in the analysis. Race and geographical origin of the accessions may be responsible for the structure we observed in our material. The extent of linkage disequilibrium for all combinations of SSRs was in agreement with expectations based on the mating system.

Genetic Diversity of a Parasitic Weed, Striga hermonthica, on Sorghum and Pearl Millet in Mali

Eleven populations of witchweed, Striga hermonthica, were collected in four regions of Mali and investigated with 12 microsatellite markers. Extensive genetic diversity was observed, with most plants heterozygous for most markers. Allelic diversity was broadly distributed across populations with little genetic differentiation and large amounts of gene flow. Nearby fields of pearl millet and sorghum were found to have indistinguishable witchweed populations. Some population structure was apparent, but did not correlate with the local environment or host genotype, suggesting that seed transportation or other human-driven variables act to differentiate central Malian S. hermonthica populations from southern Malian populations.

Helping farmers adapt to climate and cropping system change through increased access to sorghum genetic resources adapted to prevalent sorghum cropping systems in Burkina Faso

Sorghum (Sorghum bicolor (L.) Moench) is a major staple crop of Burkina Faso where farmers continue to cultivate photoperiod-sensitive guinea landraces as part of the strategy to minimize risk and ensure yield stability. In the Boucle du Mouhoun region, however, sorghum farmers appear to have insufficient varietal choice due to cropping systems having shifted towards more intensive cultivation of cotton and maize, and rainfall patterns having decreased over the past decade. In search for new varietal options that can respond to this changing context, researchers decided to give farmers access to ex-situ national collections along with the opportunity to evaluate recent improved varieties. From 2002 to 2007, researchers and farmers worked closely together to implement on-farm testing, including varietal selection trials, crop management and multi-locational trials. Farmers’ choices tend to differ among groups, villages and years, with the exception of four particular landraces: two originating from a collection carried out in the Mouhoun region more than 30 years previous to this research, and two other landraces that came from the dissimilar agro-ecological zones of Burkina Faso. These four were the most commonly selected landraces out of 36 cultivars that covered both improved and landrace varieties. Farmers’ selection criteria were focused on adaptation to agro-climatic conditions as well as specific grain qualities for processing and consumption. The potential usefulness of each variety was verified via multi-locational trials. The paper also shows that wide dissemination of experimental seed, not just across the Mouhoun region but also at a national scale, was largely achieved through collaboration with a strong farmer organisation in conjunction with farmer training programs focused on the on-farm seed production and the commercialisation of this seed.

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.