Mitochondrial DNA diversity in wild and cultivated sorghum

De novo identification and targeted sequencing of SSRs efficiently fingerprints Sorghum bicolor sub-population identity

Recent plant breeding studies of several species have demonstrated the utility of combining molecular assessments of genetic distance into trait-linked SNP genotyping during the development of parent lines to maximize yield gains due to heterosis. SSRs (Short Sequence Repeats) are the molecular marker of choice to determine genetic diversity, but the methods historically used to sequence them have been burdensome. The ability to analyze SSRs in a higher-throughput manner independent of laboratory conditions would increase their utility in molecular ecology, germplasm curation, and plant breeding programs worldwide. This project reports simple bioinformatics methods that can be used to generate genome-wide de novo SSRs in silico followed by targeted Next Generation Sequencing (NGS) validation of those that provide the most information about sub-population identity of a breeding line, which influences heterotic group selection. While these methods were optimized in sorghum [Sorghum bicolor (L.) Moench], they were developed to be applied to any species with a reference genome and high-coverage whole-genome sequencing data of individuals from the sub-populations to be characterized. An analysis of published sorghum genomes selected to represent its five main races (bicolor, caudatum, durra, kafir, and guinea; 75 accessions total) identified 130,120 SSR motifs. Average lengths were 23.8 bp and 95% were between 10 and 92 bp, making them suitable for NGS. Validation through targeted sequencing amplified 188 of 192 assayed SSR loci. Results highlighted the distinctness of accessions from the guinea sub-group margaritiferum from all other sorghum accessions, consistent with previous studies of nuclear and mitochondrial DNA. SSRs that efficiently fingerprinted margaritiferum individuals (Xgma1 -Xgma6) are presented. Developing similar fingerprints of other sub-populations (Xunr1 -Xunr182) was not possible due to the extensive admixture between them in the data set analyzed. In summary, these methods were able to fingerprint specific sub-populations when rates of admixture between them are low.

Genetic diversity of Ethiopian sorghum reveals signatures of climatic adaptation

A large collection of Ethiopian sorghum landraces, characterized by agro-ecology and racial-group, was found to contain high levels of diversity and admixture, with significant SNP associations identified for environmental adaptation. Sorghum [Sorghum bicolor L. (Moench)] is a major staple food crop in Ethiopia, exhibiting extensive genetic diversity with adaptations to diverse agroecologies. The environmental and climatic drivers, as well as the genomic basis of adaptation, are poorly understood in Ethiopian sorghum and are critical elements for the development of climate-resilient crops. Exploration of the genome-environment association (GEA) is important for identifying adaptive loci and predicting phenotypic variation. The current study aimed to better understand the GEA of a large collection of Ethiopian sorghum landraces (n = 940), characterized with genome-wide SNP markers, to investigate key traits related to adaptation to temperature, precipitation and altitude. The Ethiopian sorghum landrace collection was found to consist of 12 subpopulations with high levels of admixture (47%), representing all the major racial groups of cultivated sorghum with the exception of kafir. Redundancy analysis indicated that agroecology explained up to 10% of the total SNP variation, and geographical location up to 6%. GEA identified 18 significant SNP markers for environmental variables. These SNPs were found to be significantly enriched (P < 0.05) for a priori QTL for drought and cold adaptation. The findings from this study improve our understanding of the genetic control of adaptive traits in Ethiopian sorghum. Further, the Ethiopian sorghum germplasm collection provides sources of adaptation to harsh environments (cold and/or drought) that could be deployed in breeding programs globally for abiotic stress adaptation.

The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns

Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well-understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and nine wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a global reduction of diversity during the domestication process, although several genes also showed patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyzes revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totaling 2,449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that the combined and intricated effects of the domestication and improvement processes do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome. Overall, these analyzes pave the way toward the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.

Assessment of genetic diversity in the sorghum reference set using EST-SSR markers

Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379-0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping.

Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources

Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated. Except for Kafir, there was little correspondence between races and marker-based groups. Bicolor, Caudatum, Durra and Guinea types were each dispersed in three groups or more. Races should therefore better be referred to as morphotypes. Wild and weedy accessions were very diverse and scattered among cultivated samples, reinforcing the idea that large gene-flow exists between the different compartments. Our study provides an entry to global sorghum germplasm collections. Our reference marker kit can serve to aggregate additional studies and enhance international collaboration. We propose a core reference set in order to facilitate integrated phenotyping experiments towards refined functional understanding of sorghum diversity.

Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild-weedy-crop complex in a western African region

Gene flow between domesticated plants and their wild relatives is one of the major evolutionary processes acting to shape their structure of genetic diversity. Earlier literature, in the 1970s, reported on the interfertility and the sympatry of wild, weedy and cultivated sorghum belonging to the species Sorghum bicolor in most regions of sub-Saharan Africa. However, only a few recent surveys have addressed the geographical and ecological distribution of sorghum wild relatives and their genetic structure. These features are poorly documented, especially in western Africa, a centre of diversity for this crop. We report here on an exhaustive in situ collection of wild, weedy and cultivated sorghum assembled in Mali and in Guinea. The extent and pattern of genetic diversity were assessed with 15 SSRs within the cultivated pool (455 accessions), the wild pool (91 wild and weedy forms) and between them. F (ST) and R (ST) statistics, distance-based trees, Bayesian clustering methods, as well as isolation by distance models, were used to infer evolutionary relationships within the wild-weedy-crop complex. Firstly, our analyses highlighted a strong racial structure of genetic diversity within cultivated sorghum (F (ST) = 0.40). Secondly, clustering analyses highlighted the introgressed nature of most of the wild and weedy sorghum and grouped them into two eco-geographical groups. Such closeness between wild and crop sorghum could be the result of both sorghum's domestication history and preferential post-domestication crop-to-wild gene flow enhanced by farmers' practices. Finally, isolation by distance analyses showed strong spatial genetic structure within each pool, due to spatially limited dispersal, and suggested consequent gene flow between the wild and the crop pools, also supported by R (ST) analyses. Our findings thus revealed important features for the collection, conservation and biosafety of domesticated and wild sorghum in their centre of diversity.

Genetic structure and relationships within and between cultivated and wild sorghum (Sorghum bicolor (L.) Moench) in Kenya as revealed by microsatellite markers

Understanding the extent and partitioning of diversity within and among crop landraces and their wild/weedy relatives constitutes the first step in conserving and unlocking their genetic potential. This study aimed to characterize the genetic structure and relationships within and between cultivated and wild sorghum at country scale in Kenya, and to elucidate some of the underlying evolutionary mechanisms. We analyzed at total of 439 individuals comprising 329 cultivated and 110 wild sorghums using 24 microsatellite markers. We observed a total of 295 alleles across all loci and individuals, with 257 different alleles being detected in the cultivated sorghum gene pool and 238 alleles in the wild sorghum gene pool. We found that the wild sorghum gene pool harbored significantly more genetic diversity than its domesticated counterpart, a reflection that domestication of sorghum was accompanied by a genetic bottleneck. Overall, our study found close genetic proximity between cultivated sorghum and its wild progenitor, with the extent of crop-wild divergence varying among cultivation regions. The observed genetic proximity may have arisen primarily due to historical and/or contemporary gene flow between the two congeners, with differences in farmers' practices explaining inter-regional gene flow differences. This suggests that deployment of transgenic sorghum in Kenya may lead to escape of transgenes into wild-weedy sorghum relatives. In both cultivated and wild sorghum, genetic diversity was found to be structured more along geographical level than agro-climatic level. This indicated that gene flow and genetic drift contributed to shaping the contemporary genetic structure in the two congeners. Spatial autocorrelation analysis revealed a strong spatial genetic structure in both cultivated and wild sorghums at the country scale, which could be explained by medium- to long-distance seed movement.

[Molecular phylogenetic relationships among species in the genus Sorghum based on partial Adh1 gene]

The genus Sorghum contains some important grain crops and economically important forage grasses as well as agricultural weeds. The goals of this study were to elucidate the phylogenetic relationships between Sorghum species and ascertain the taxonomy status of the quarantine weeds which provide bases for effective utilization of its germ resources on molecular breeding and improvement of crop qualities and thus provide important guidance for port detection. In the present study, total DNA from the seeds of 8 Sorghum species (four S. almum, two S. halepense, one S. silk and one S. sudanense)were extracted, and the partial Adh1 gene of about 2,000 bp in length were amplified by PCR using specific primers designed from conserved regions of Adh1 gene reported in the GenBank (AF050456) and sequenced. Based on these sequences and other 24 Adh1 sequences registered in the GenBank, the phylogenetic trees constructed by multiple methods (MP, ML, and NJ) with the corresponding Adh1 sequence of Cleistachne sorghoides as the outgroup shared almost the same topology. The results showed that: (1) there were obviously three lineages for the genus Sorghum. One included two subgenera Chaetosorghum and Heterosorghum, and another included subgenus Eusorghum, both of which consisted of 2n=20 and 2n=40 species with small chromosomes. Still another lineage contained the two subgenera Parasorghum and Stiposorghum with 2n=10 species and their polyploid relatives with relatively large chromosomes; (2) geographical divergence clearly existed in the S. almum; (3) S. purpureosericeum, S. versicolor, S. nitidum and S. leiocladum of subgenus Parasorghum clustered together, but S. matarankense, S. grande, and S. timorense of the same subgenus clustered with the species of subgenus Stiposorghum, showing closer relationship with subgenus Stiposorghum; (4) S. macrospermum was more closely related to S. laxiflorum than the other species of the genus Sorghum.

Phylogeographic evidence of crop neodiversity in sorghum

Sorghum has shown the adaptability necessary to sustain its improvement during time and geographical extension despite a genetic foundation constricted by domestication bottlenecks. Initially domesticated in the northeastern part of sub-Saharan Africa several millenia ago, sorghum quickly spread throughout Africa, and to Asia. We performed phylogeographic analysis of sequence diversity for six candidate genes for grain quality (Shrunken2, Brittle2, Soluble starch synthaseI, Waxy, Amylose extender1, and Opaque2) in a representative sample of sorghum cultivars. Haplotypes along 1-kb segments appeared little affected by recombination. Sequence similarity enabled clustering of closely related alleles and discrimination of two or three distantly related groups depending on the gene. This scheme indicated that sorghum domestication involved structured founder populations, while confirming a specific status for the guinea margaritiferum subrace. Allele rooted genealogy revealed derivation relationships by mutation or, less frequently, by recombination. Comparison of germplasm compartments revealed contrasts between genes. Sh2, Bt2, and SssI displayed a loss of diversity outside the area of origin of sorghum, whereas O2 and, to some extent, Wx and Ae1 displayed novel variation, derived from postdomestication mutations. These are likely to have been conserved under the effect of human selection, thus releasing valuable neodiversity whose extent will influence germplasm management strategies.

Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers

Understanding the geographical, environmental and social patterns of genetic diversity on different spatial scales is key to the sustainable in situ management of genetic resources. However, few surveys have been conducted on crop genetic diversity using exhaustive in situ germplasm collections on a country scale and such data are missing for sorghum in sub-Saharan Africa, its centre of origin. We report here a genetic analysis of 484 sorghum varieties collected in 79 villages evenly distributed across Niger, using 28 microsatellite markers. We found a high level of SSR diversity in Niger. Diversity varied between eastern and western Niger, and allelic richness was lower in the eastern part of the country. Genetic differentiation between botanical races was the first structuring factor (Fst = 0.19), but the geographical distribution and the ethnic group to which farmers belonged were also significantly associated with genetic diversity partitioning. Gene pools are poorly differentiated among climatic zones. The geographical situation of Niger, where typical western African (guinea), central African (caudatum) and eastern Sahelian African (durra) sorghum races converge, explained the high observed genetic diversity and was responsible for the interactions among the ethnic, geographical and botanical structure revealed in our study. After correcting for the structure of botanical races, spatial correlation of genetic diversity was still detected within 100 km, which may hint at limited seed exchanges between farmers. Sorghum domestication history, in relation to the spatial organisation of human societies, is therefore key information for sorghum in situ conservation programs in sub-Saharan Africa.

Evaluation of genetic variability of sorghum (Sorghum bicolor L. Moench) in northwestern Morocco by ISSR and RAPD markers

The study of the genetic variability of the Moroccan landraces of sorghum constitutes a necessary step that can be exploited in the programs of improvement and valorisation of this marginalized species. The aim of this investigation is to evaluate the variability of sorghum populations and to establish their phylogenetic relations using RAPD and ISSR markers. Sampling was taken in 33 fields of northern regions where this species is most cultivated. Individual plants (398) were collected in 13, 11, 5, and 4 fields of Larache, Tangier, Chefchaouen, and Tetouan, respectively. Thirty-eight RAPD primers and four ISSR primers were used. The percentage of polymorphic fragments revealed with ISSR (98%) is higher than the one revealed with RAPD (85%). The level of the variability obtained through the two techniques is very high. Nevertheless, ISSR markers revealed more diversity than RAPD (0.995+/-0.006 against 0.946+/-0.031). The classification based on Jaccard's similarity index distinguished the totality of fields. Data analysis revealed a genetic structure that is closely related to the micro-geographical repartition of the different fields.

A global view of genetic diversity in cultivated sorghums using a core collection

We report here an analysis of the structure of genetic diversity in cultivated sorghums. A core collection of 210 landraces representative of race, latitude of origin, response to day length, and production system was analysed with 74 RFLP probes dispersed throughout the genome. Multivariate analyses showed the specificity of the subrace guinea margaritiferum, as well as the geographical and racial pattern of genetic diversity. Neighbour-joining analysis revealed a clear differentiation between northern and southern equatorial African accessions. The presence of Asian accessions in these 2 major geographical poles for sorghum evolution indicated two introductions of sorghum into Asia. Morphological race also influenced the pattern of sorghum genetic diversity. A single predominant race was identified in 8 of 10 clusters of accessions, i.e., 1 kafir, 1 durra, 4 guinea, and 2 caudatum clusters. Guinea sorghums, with the exception of accessions in the margaritiferum subrace, clustered in 3 geographical groups, i.e., western African, southern African, and Asian guinea clusters; the latter two appeared more closely related. Caudatum were mainly distributed in 2 clusters, the African Great Lakes caudatum cluster and those African caudatum originating from other African regions. This last differentiation appears related to contrasting photoperiod responses. These results aid in the optimization of sampling accessions for introgression in breeding programs.

The pattern of genetic diversity of Guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers

The Guinea-race of sorghum [Sorghum bicolor (L.) Moench] is a predominantly inbreeding, diploid cereal crop. It originated from West Africa and appears to have spread throughout Africa and South Asia, where it is now the dominant sorghum race, via ancient trade routes. To elucidate the genetic diversity and differentiation among Guinea-race sorghum landraces, we selected 100 accessions from the ICRISAT sorghum Guinea-race Core Collection and genotyped these using 21 simple sequence repeat (SSR) markers. The 21 SSR markers revealed a total of 123 alleles with an average Dice similarity coefficient of 0.37 across 4,950 pairs of accessions, with nearly 50% of the alleles being rare among the accessions analysed. Stratification of the accessions into 11 countries and five eco-regional groups confirmed earlier reports on the spread of Guinea-race sorghum across Africa and South Asia: most of the variation was found among the accessions from semi-arid and Sahelian Africa and the least among accessions from South Asia. In addition, accessions from South Asia most closely resembled those from southern and eastern Africa, supporting earlier suggestions that sorghum germplasm might have reached South Asia via ancient trade routes along the Arabian Sea coasts of eastern Africa, Arabia and South Asia. Stratification of the accessions according to their Snowden classification indicated clear genetic variation between margeritiferum, conspicuum and Roxburghii accessions, whereas the gambicum and guineënse accessions were genetically similar. The implications of these findings for sorghum Guinea-race plant breeding activities are discussed.

Abundant mitochondrial genome diversity, population differentiation and convergent evolution in pines

We examined mitochondrial DNA polymorphisms via the analysis of restriction fragment length polymorphisms in three closely related species of pines from western North America: knobcone (Pinus attenuata Lemm.), Monterey (P. radiata D. Don), and bishop (P. muricata D. Don). A total of 343 trees derived from 13 populations were analyzed using 13 homologous mitochondrial gene probes amplified from three species by polymerase chain reaction. Twenty-eight distinct mitochondrial DNA haplotypes were detected and no common haplotypes were found among the species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (HS) averaged 0.22, and population differentiation (GST and theta) exceeded 0.78. Analysis of molecular variance also revealed that >90% of the variation resided among populations. For the purposes of genetic conservation and breeding programs, species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Neighbor-joining phenograms, however, strongly disagreed with those based on allozymes, chloroplast DNA, and morphological traits. Thus, despite its diagnostic haplotypes, the genome appears to evolve via the rearrangement of multiple, convergent subgenomic domains.

Phylogenetic relationships of sorghum taxa inferred from mitochondrial DNA restriction fragment analysis

To elucidate the evolutionary history and affinity of sorghum species, 41 sorghum taxa were analyzed using variability in mitochondrial DNA. Analysis of species relationships at the molecular level can provide additional data to supplement the existing classification based on morphological characters and may also furnish unexpected but useful information. Total DNA extracted from each of the sorghum accessions was digested with each of five restriction enzymes, BamHI, HindIII, EcoRI, EcoRV, and XbaI, and probed with five mitochondrial DNAs cloned from Sorghumbicolor. A total of 180 restriction fragments was detected by the 25 probe–enzyme combinations. Forty-three fragment bands were phylogenetically informative. Multiple correspondence analysis was performed to visualize associations among the accessions and suggested that section Eusorghum species may be divided into four groups, with Sorghumlaxiflorum (section Heterosorghum) and Sorghumnitidum (section Parasorghum) appearing as outliers. A phylogenetic tree was assembled from mitochondrial restriction fragment data. The taxa analyzed formed three major groups comprising section Heterosorghum (group I), section Parasorghum (group II), and all accessions in section Eusorghum (group III). Group III is further divided into four groups: (i) two sweet sorghums and shattercane; (ii) Sorghumhalepense, Sorghummiliaceum, Sorghumhewisonii, Sorghumaethiopicum, Sorghumverticilliflorum, and S. bicolor, including Sorghumsudanense (sudangrass), the Chinese Kaoliangs, and a number of commercial sorghum inbreds from the U.S.A.; (iii) Sorghumpropinquum; and (iv) Sorghumarundinaceum, Sorghumniloticum, Sorghumalmum, Sorghumcontroversum, and the Chinese material C-401 and 5-27. Results indicate that the analysis of fragmented mitochondrial DNA was diagnostic and useful in sorghum phylogenetic and taxonomic research at the species, subspecies, and race levels, and can complement results from those analyses using nuclear ribosomal DNA and chloroplast DNA that effectively distinguish taxa at species and genus levels. Key words : Sorghum, mitochondrial DNA, phylogeny, restriction fragment.