Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild�Cweedy�Ccrop 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.     

Local scale patterns of gene flow and genetic diversity in a crop–wild–weedy complex of sorghum (Sorghum bicolor (L.) Moench) under traditional agricultural field conditions in Kenya

Little information is available on the extent and patterns of gene flow and genetic diversity between cultivated sorghum and its wild related taxa under local agricultural conditions in Africa. As well as expanding knowledge on the evolutionary and domestication processes for sorghum, such information also has importance in biosafety, conservation and breeding programmes. Here, we examined the magnitude and dynamics of crop–wild gene flow and genetic variability in a crop–wild–weedy complex of sorghum under traditional farming in Meru South district, Kenya. We genotyped 110 cultivated sorghum, and 373 wild sorghum individuals using a panel of ten polymorphic microsatellite loci. We combined traditional measures of genetic diversity and differentiation with admixture analysis, population assignment, and analyses of spatial genetic structure to assess the extent and patterns of gene flow and diversity between cultivated and wild sorghum. Our results indicate that gene flow is asymmetric with higher rates from crop to wild forms than vice versa. Surprisingly, our data suggests that the two congeners have retained substantial genetic distinctness in the face of gene flow. Nevertheless, we found no significant differences in genetic diversity measures between them. Our study also did not find evidence of isolation by distance in cultivated or wild sorghum, which suggests that gene dispersal in the two conspecifics is not limited by geographic distance. Overall our study highlights likely escape and dispersal of transgenes within the sorghum crop–wild–weedy complex if genetically engineered varieties were to be introduced in Africa’s traditional farming systems.     

Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation

The small genome of sorghum (Sorghum bicolor L. Moench.) provides an important template for study of closely related large-genome crops such as maize (Zea mays) and sugarcane (Saccharum spp.), and is a logical complement to distantly related rice (Oryza sativa) as a "grass genome model." Using a high-density RFLP map as a framework, a robust physical map of sorghum is being assembled by integrating hybridization and fingerprint data with comparative data from related taxa such as rice and using new methods to resolve genomic duplications into locus-specific groups. By taking advantage of allelic variation revealed by heterologous probes, the positions of corresponding loci on the wheat (Triticum aestivum), rice, maize, sugarcane, and Arabidopsis genomes are being interpolated on the sorghum physical map. Bacterial artificial chromosomes for the small genome of rice are shown to close several gaps in the sorghum contigs; the emerging rice physical map and assembled sequence will further accelerate progress. An important motivation for developing genomic tools is to relate molecular level variation to phenotypic diversity. "Diversity maps," which depict the levels and patterns of variation in different gene pools, shed light on relationships of allelic diversity with chromosome organization, and suggest possible locations of genomic regions that are under selection due to major gene effects (some of which may be revealed by quantitative trait locus mapping). Both physical maps and diversity maps suggest interesting features that may be integrally related to the chromosomal context of DNA-progress in cytology promises to provide a means to elucidate such relationships. We seek to provide a detailed picture of the structure, function, and evolution of the genome of sorghum and its relatives, together with molecular tools such as locus-specific sequence-tagged site DNA markers and bacterial artificial chromosome contigs that will have enduring value for many aspects of genome analysis.     

Host-plant preference and oviposition responses of the sorghum midge, Stenodiplosis sorghicola (Coquillett) (Dipt., Cecidomyiidae) towards wild relatives of sorghum

Sorghum midge, Stenodiplosis ( Contarinia ) sorghicola (Coquillett) is an important pest of grain sorghum world-wide. Considerable progress has been made in screening and breeding for resistance to sorghum midge. However, some of the sources of resistance have become susceptible to sorghum midge in Kenya, in eastern Africa. Therefore, the wild relatives of Sorghum bicolor were studied as a possible source of new genes conferring resistance to sorghum midge. Midge females did not lay eggs in the spikelets of Sorghum amplum , Sorghum bulbosum , and Sorghum angustum compared to 30% spikelets with eggs in Sorghum halepense when infested with five midge females per panicle under no-choice conditions. However, one egg was laid in S. amplum when infested with 50 midges per panicle. A larger number of midges were attracted to the odours from the panicles of S. halepense than to the panicles of Sorghum stipoideum , Sorghum brachypodum , S. angustum , Sorghum macrospermum , Sorghum nitidium , Sorghum laxiflorum , and S. amplum in dual-choice olfactometer tests. The differences in midge response to the odours from S. halepense and Sorghum intrans were not significant. Under multi-choice conditions, when the females were also allowed a contact with the host, more sorghum midge females were attracted to the panicles of S. bicolor compared with S. amplum , S. angustum , and S. halepense . In another test, numerically more midges responded to the panicles of IS 10712 compared with S. halepense , whereas the differences in midge response to the panicles of ICSV 197 ( S. bicolor ) and S. halepense were not apparent, indicating that S. halepense is as attractive to sorghum midge females as S. bicolor . The wild relatives of sorghum (except S. halepense ) were not preferred for oviposition, and they were also less attractive to the sorghum midge females. Thus, wild relatives of sorghum can prove to be an alternative source of genes for resistance to sorghum midge.     

Gene Flow and its Consequences in Sorghum spp.

Gene flow between crops and their weedy or wild relatives can be problematic in modern agricultural systems, especially if it endows novel adaptive genes that confer tolerance to abiotic and biotic stresses. Alternatively, gene flow from weedy relatives to domesticated crops may facilitate ferality through introgression of weedy characteristics in the progeny. Cultivated sorghum (Sorghum bicolor), is particularly vulnerable to the risks associated with gene flow to several weedy relatives, johnsongrass (S. halepense), shattercane (S. bicolor ssp. drummondii) and columbusgrass (S. almum). Johnsongrass and shattercane are common weeds in many sorghum production areas around the world. Sorghum varieties with adaptive traits developed through conventional breeding or novel transgenesis pose agronomic and ecological risks if transferred into weedy/wild relatives. Knowledge of the nature and characteristics of gene flow among different sorghum species is scarce, and existing knowledge is scattered. Here, we review current knowledge of gene flow between cultivated sorghum and its weedy and wild relatives. We further discuss potential avenues for addressing gene flow through genetic, molecular, and field level containment, mitigation and management strategies to facilitate successful deployment of novel traits in this economically important crop species.     

Genetic structure and relationships within and between cultivated and wild sorghum (<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (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.     

Advances in Arachis genomics for peanut improvement

Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.     

高粱遗传转化研究进展

高粱（Sorghum bicolor）是一种重要的多用途作物, 其遗传转化研究对于高粱的分子育种和分子遗传学基础研究都具有重要意义。该文对高粱遗传转化的方法、标记基因、遗传转化的启动子和受体系统进行了综述, 并提出了今后高粱遗传转化应当集中研究的问题。     

Assessment of genetic diversity among sorghum landraces and their wild/weedy relatives in western Kenya using simple sequence repeat (SSR) markers

Understanding the extent of gene exchange between cultivated sorghum and its wild/weedy relatives and the evolutionary processes (including farmers’ practices) that act to shape the structure of genetic diversity within and between them is an important aspect for germplasm conservation strategies, biosafety risk assessment, and crop improvement programs. In this study, molecular characterization and genetic diversity analyses were conducted on wild, weedy and cultivated sorghums collected at a local-scale in a traditional farming system in the Lambwe Valley of western Kenya. Nine simple sequence repeat (SSR) markers were used to genotype 294 cultivated sorghum and 200 wild sorghum individuals. The nine SSR markers were highly polymorphic with a number of alleles that varied from 2 to 19. Overall, wild sorghums had higher genetic diversity, observed heterozygosity, total number of alleles, polymorphic information content and more genotypes per locus than the cultivated types. A Mantel test demonstrated that there was significant isolation-by-distance for wilds and cultivated materials. STRUCTURE, cluster and principal coordinate analyses consistently assigned wild and cultivated individuals to different groups but failed to place hybrids/weedy types as a single separate group from wilds. Our results provide strong evidence of significant genetic diversity retained within wilds, larger divergence between wild and cultivated materials and reduced gene flow than those previously reported in Kenya. These results demonstrate the value of the Lambwe Valley region as a genetic reservoir and the importance to conduct genetic diversity studies at the local scale to design and execute appropriate in situ conservation programs and policies.     

A Diploid,Interspecific, Fertile Hybrid from Cultivated Sorghum, <Emphasis Type="Italic">Sorghum Bicolor</Emphasis>, and the Common Johnsongrass Weed <Emphasis Type="Italic">Sorghum Halepense</Emphasis>

Valuable agronomic traits are often present but inaccessible in the wild relatives of cultivated crop species. Utilization of wild germplasm depends on the production of fertile interspecific hybrids. Several unsuccessful attempts have been made to hybridize cultivated sorghum with its wild relatives to broaden its genetic base and enhance agronomic value. The successful approach used in this study employed the nuclear male sterility gene ms3 to generate a diploid fertile hybrid between the diploid cultivated sorghum (Sorghum bicolor (L) Pers.) and its weedy tetraploid wild relative Johnsongrass (Sorghum halepense (L.) Pers.). Eight sorghum plants were selected from a Nebraska stiff stalk collection that contains the male sterility gene ms3 and were used as the female parent. About 36,000 florets of male sterile sorghum were pollinated with Johnsongrass pollen to produce an average of one well-developed and 180 severely shriveled seed/18,000 crosses. The well-developed seed gave rise to a self-fertile diploid, while none of the shriveled seed were able to germinate. The F₁ hybrid was confirmed by using cultivated sorghum SSR markers and was selfed to produce an F₂ population. A sub-sample of 96 segregating F₂ plants was examined with 36 sorghum polymorphic SSR markers. Thirty-four markers showed a normal 1:2:1 segregation ratio, evidence of normal recombination across the genome. Preliminary results showed that several desirable traits from Johnsongrass, including resistance to greenbug and chinch bug and adaptability to cold temperatures, were expressed in the resulting progenies. These observations suggest that speciation within the genus Sorghum, giving rise to widely divergent phenotypes, is effected largely by ploidy-maintained crossing barriers but apparently not by extensive genomic divergence.     

高梁基因组学研究的新进展

高梁是全球第五大禾谷类作物,在干旱、半干旱地区农业生产中占有权其重要的位置。高梁基因组相对较小(750Mbp),遗传多样性丰富,被认为是禾谷类作物比较基因组学研究的模式基因组之一。近年来,综合运用AFLP等分子标记、BAC文库、EST及cDNA作图和FIsH技术,加速了高梁高分辨率基因组图谱的构建。高梁基因测序、基因功能鉴定和克隆,以及遗传转化,亦取得了长足的进展。高梁特有的多种适应逆境胁迫等优异基因资源的发掘及其在作物改良中的应用前景广阔。     

Molecular genetic analysis of soriz genome (Sorghum oryzoidum)

Molecular-genetic analysis of soriz genotypes (Sorghum oryzoidum), its paternal form Sorghum bicolor (L.) Moench (grain sorghum), possible parents (Sorghum sudanense (Piper.) Stapf. (Sudan grass) and Oryza sativa L. (rice planting)) and the nearest relatives has been carried out using microsatellite (MS) loci of sorghum and rice. Based on these data genetic distances have been calculated. It was shown that soriz do not bear DNA fragments of rice, but contains in its genome DNA fragments belonging to the Sudanese grass indicating that the origin of soriz is associated with Sorghum sudanense.     

Genetic diversity of sorghum accessions resistant to greenbugs as assessed with AFLP markers.

Sorghum, Sorghum bicolor (L.) Moench, is the fifth most important cereal crop grown worldwide and the fourth in the United States. Greenbug, Schizaphis graminum (Rondani), is a major insect pest of sorghum with several biotypes reported to date. Greenbug biotype I is currently the most prevalent and most virulent on sorghum plants. Breeding for resistance is an effective way to control greenbug damage. A successful breeding program relies in part upon a clear understanding of breeding materials. However, the genetic diversity and relatedness among the greenbug biotype I resistant accessions collected from different geographic origins have not been well characterized, although a rich germplasm collection is available. In this study, 26 sorghum accessions from 12 countries were evaluated for both resistance to greenbug biotype I and genetic diversity using fluorescence-labeled amplified fragment length polymorphism (AFLP). Twenty-six AFLP primer combinations produced 819 polymorphic fragments indicating a relatively high level of polymorphism among the accessions. Genetic similarity coefficients among the sorghum accessions ranged from 0.69 to 0.90. Cluster analysis indicated that there were two major groups based on polymorphic bands. This study has led to the identification of new genetic sources of sorghum with substantial genetic variation and distinct groupings of resistant accessions that have the potential for use in the development of durable greenbug resistant sorghum.     

Lack of low frequency variants masks patterns of non-neutral evolution following domestication

Detecting artificial selection in the genome of domesticated species can not only shed light on human history but can also be beneficial to future breeding strategies. Evidence for selection has been documented in domesticated species including maize and rice, but few studies have to date detected signals of artificial selection in the Sorghum bicolor genome. Based on evidence that domesticated S. bicolor and its wild relatives show significant differences in endosperm structure and quality, we sequenced three candidate seed storage protein (kafirin) loci and three candidate starch biosynthesis loci to test whether these genes show non-neutral evolution resulting from the domestication process. We found strong evidence of non-neutral selection at the starch synthase IIa gene, while both starch branching enzyme I and the beta kafirin gene showed weaker evidence of non-neutral selection. We argue that the power to detect consistent signals of non-neutral selection in our dataset is confounded by the absence of low frequency variants at four of the six candidate genes. A future challenge in the detection of positive selection associated with domestication in sorghum is to develop models that can accommodate for skewed frequency spectrums.     

Genome-wide patterns of large-size presence/absence variants in sorghum

The presence/absence variants （PAVs） are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum （Sorghum bicolour L.） genomes, each 12？ coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size （＆gt;30 kb） PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode celldeath and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA trans-posons as the major components. The frequency and distribution of these PAVs differed substantial y across 96＆amp;nbsp;sorghum inbred lines, and the low-and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.     

Genetic structure and diversity of wild sorghum populations (<Emphasis Type="Italic">Sorghum</Emphasis> spp.) from different eco-geographical regions of Kenya

Wild sorghums are extremely diverse phenotypically, genetically and geographically. However, there is an apparent lack of knowledge on the genetic structure and diversity of wild sorghum populations within and between various eco-geographical regions. This is a major obstacle to both their effective conservation and potential use in breeding programs. The objective of this study was to assess the genetic diversity and structure of wild sorghum populations across a range of eco-geographical conditions in Kenya. Sixty-two wild sorghum populations collected from the 4 main sorghum growing regions in Kenya were genotyped using 18 simple sequence repeat markers. The study showed that wild sorghum is highly variable with the Coast region displaying the highest diversity. Analysis of molecular variance showed a significant variance component within and among wild sorghum populations within regions. The genetic structure of wild sorghum populations indicated that gene flow is not restricted to populations within the same geographic region. A weak regional differentiation was found among populations, reflecting human intervention in shaping wild sorghum genetic structure through seed-mediated gene flow. The sympatric occurrence of wild and cultivated sorghums coupled with extensive seed-mediated gene flow, suggests a potential crop-to-wild gene flow and vice versa across the regions. Wild sorghum displayed a mixed mating system. The wide range of estimated outcrossing rates indicate that some environmental conditions may exist where self-fertilisation is favoured while others cross-pollination is more advantageous.     

Restriction fragment variation in the nuclear and chloroplast genomes of cultivated and wild Sorghum bicolor

Summary Fifty-six accessions of cultivated and wild sorghum were surveyed for genetic diversity using 50 low-copy-number nuclear DNA sequence probes to detect restriction fragment length polymorphisms (RFLPs). These probes revealed greater genetic diversity in wild sorghum than in cultivated sorghum, including a larger number of alleles per locus and a greater portion of polymorphic loci in wild sorghum. In comparison to previously published isozyme analyses of the same accessions, RFLP analysis reveals a greater number of alleles per locus. Furthermore, many RFLP alleles have frequencies between 0.25–0.75, while the vast majority of isozyme alleles are either rare (< 0.25) or near fixation (> 0.75). Correlations between genetic and geographic distances among the accessions were stronger when calculated with RFLP than with isozyme data. Systematic relationships revealed by nuclear and chloroplast restriction site analysis indicate that cultivated sorghum is derived from the wild ssp. arundinaceum. The portion of the wild gene pool most genetically similar to the cultivars is from central-northeastern Africa. Previous published data also suggested that this is most likely the principal area of domestication of sorghum. Introgression between wild and cultivated sorghum was inferred from disconcordant relationships shown by nuclear and chloroplast DNA markers. Introgression apparently occurs infrequently enough that the crop and its wild relatives maintain distinct genetic constitutions.     

Molecular evolution of the phytochrome gene family in sorghum: changing rates of synonymous and replacement evolution

The photoreceptor phytochromes, encoded by a small gene family, are responsible for controlling the expression of a number of light-responsive genes and photomorphogenic events, including agronomically important phenotypes such as flowering time and shade-avoidance behavior. The understanding and control of flowering time are particularly important goals in sorghum cultivar development for diverse environments, and naturally occurring variation in the phytochrome genes might prove useful in breeding programs. Also of interest is whether variation observed at the phytochrome loci in domesticated sorghum, or in particular races, is a result of human selection. Population genetic studies can reveal evidence of such selection in patterns of polymorphism and divergence. In this study we report a population genetic analysis of the PHY gene family in Sorghum bicolor (L.) Moench in a diverse panel including both cultivated and wild accessions. We show that the level of nucleotide variation in all gene family members is about half the average for this species, consistent with purifying selection acting on these loci. However, the rate of amino acid substitution is accelerated at PHYC compared to the other two loci. In comparisons to a closely related sorghum species, PHYC shows a pattern of intermediate frequency amino acid changes that differ from the patterns observed in comparisons across longer evolutionary distances. There is also a departure from expected patterns of polymorphism and divergence at synonymous sites in PHYC, although the data do not fit a simple model of directional or diversifying selection. Cultivated sorghum has a level of variation similar to that of wild relatives (ssp. verticilliflorum), but many polymorphisms are subspecies-specific, including several amino acid variants.     

Biotechnology: Genetic improvement of sorghum (Sorghum bicolor (L.) Moench)

Summary This report reviews the contributions to the improvement of sorghum (Sorghum bicolor (L.) Moench) through traditional approaches with emphasis on the application of biotechnological methods. Strategies include breeding for higher yield, improved grain quality, and biotic and abiotic stress tolerance. Hybrid development and polyploidy breeding are also discussed. Plant breeders, working in concert with biotechnologists, have developed new powerful tools for plant genetic manipulation and genotype evaluation that will significantly improve the efficiency of plant breeding. Improving sorghum through biotechnology is the latest in a long series of technologies that have been applied to this crop. Five basic tools of technology have been developed for sorghum improvement: (1) in vitro protocols for efficient plant regeneration; (2) molecular markers; (3) gene identification and cloning; (4) genetic engineering and gene transfer technology to integrate desirable traits into the sorghum genome; and (5) genomics and germplasm databases. Reports on studies involving the problems, progress, and prospects for utilizing the biotechnological methods for sorghum improvement are discussed.