Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes.

Quantitative trait loci (QTLs) affecting plant height and flowering were studied in the two Saccharum species from which modern sugarcane cultivars are derived. Two segregating populations derived from interspecific crosses between Saccharum officinarum and Saccharum spontaneum were genotyped with 735 DNA markers. Among the 65 significant associations found between these two traits and DNA markers, 35 of the loci were linked to sugarcane genetic maps and 30 were unlinked DNA markers. Twenty-one of the 35 mapped QTLs were clustered in eight genomic regions of six sugarcane homologous groups. Some of these could be divergent alleles at homologous loci, making the actual number of genes implicated in these traits much less than 35. Four QTL clusters controlling plant height in sugarcane corresponded closely to four of the six plant-height QTLs previously mapped in sorghum. One QTL controlling flowering in sugarcane corresponded to one of three flowering QTLs mapped in sorghum. The correspondence in locations of QTLs affecting plant height and flowering in sugarcane and sorghum reinforce the notion that the simple sorghum genome is a valuable "template" for molecular dissection of the much more complex sugarcane genome.     

Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods

The productivity of sorghum is mainly determined by agronomically important traits. The genetic bases of these traits have historically been dissected and analysed through quantitative trait locus (QTL) mapping based on linkage maps with low-throughput molecular markers, which is one of the factors that hinder precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, an ultra-high-density linkage map based on high-quality single nucleotide polymorphisms (SNPs) generated from low-coverage sequences (~0.07 genome sequence) in a sorghum recombinant inbred line (RIL) population was constructed through new sequencing technology. This map consisted of 3418 bin markers and spanned 1591.4 cM of genome size with an average distance of 0.5 cM between adjacent bins. QTL analysis was performed and a total of 57 major QTLs were detected for eight agronomically important traits under two contrasting photoperiods. The phenotypic variation explained by individual QTLs varied from 3.40% to 33.82%. The high accuracy and quality of this map was evidenced by the finding that genes underlying two cloned QTLs, Dw3 for plant height (chromosome 7) and Ma1 for flowering time (chromosome 6), were localized to the correct genomic regions. The close associations between two genomic regions on chromosomes 6 and 7 with multiple traits suggested the existence of pleiotropy or tight linkage. Several major QTLs for heading date, plant height, numbers of nodes, stem diameter, panicle neck length, and flag leaf width were detected consistently under both photoperiods, providing useful information for understanding the genetic mechanisms of the agronomically important traits responsible for the change of photoperiod.     

Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production

Background

Sorghum is a tropical C₄ cereal that recently adapted to temperate latitudes and mechanized grain harvest through selection for dwarfism and photoperiod-insensitivity. Quantitative trait loci for these traits have been introgressed from a dwarf temperate donor into hundreds of diverse sorghum landraces to yield the Sorghum Conversion lines. Here, we report the first comprehensive genomic analysis of the molecular changes underlying this adaptation.

Results

We apply genotyping-by-sequencing to 1,160 Sorghum Conversion lines and their exotic progenitors, and map donor introgressions in each Sorghum Conversion line. Many Sorghum Conversion lines carry unexpected haplotypes not found in either presumed parent. Genome-wide mapping of introgression frequencies reveals three genomic regions necessary for temperate adaptation across all Sorghum Conversion lines, containing the Dw1, Dw2, and Dw3 loci on chromosomes 9, 6, and 7 respectively. Association mapping of plant height and flowering time in Sorghum Conversion lines detects significant associations in the Dw1 but not the Dw2 or Dw3 regions. Subpopulation-specific introgression mapping suggests that chromosome 6 contains at least four loci required for temperate adaptation in different sorghum genetic backgrounds. The Dw1 region fractionates into separate quantitative trait loci for plant height and flowering time.

Conclusions

Generating Sorghum Conversion lines has been accompanied by substantial unintended gene flow. Sorghum adaptation to temperate-zone grain production involves a small number of genomic regions, each containing multiple linked loci for plant height and flowering time. Further characterization of these loci will accelerate the adaptation of sorghum and related grasses to new production systems for food and fuel.     

Comparative Genome Mapping of Sorghum and Maize

Linkage relationships were determined among 85 maize low copy number nuclear DNA probes and seven isozyme loci in an F2 population derived from a cross of Sorghum bicolor ssp. bicolor x S. bicolor ssp. arundinaceum. Thirteen linkage groups were defined, three more than the 10 chromosomes of sorghum. Use of maize DNA probes to produce the sorghum linkage map allowed us to make several inferences concerning processes involved in the evolutionary divergence of the maize and sorghum genomes. The results show that many linkage groups are conserved between these two genomes and that the amount of recombination in these conserved linkage groups is roughly equivalent in maize and sorghum. Estimates of the proportions of duplicated loci suggest that a larger proportion of the loci are duplicated in the maize genome than in the sorghum genome. This result concurs with a prior estimate that the nuclear DNA content of maize is three to four times greater than that of sorghum. The pattern of conserved linkages between maize and sorghum is such that most sorghum linkage groups are composed of loci that map to two maize chromosomes. This pattern is consistent with the hypothesized ancient polyploid origin of maize and sorghum. There are nine cases in which locus order within shared linkage groups is inverted in sorghum relative to maize. These may have arisen from either inversions or intrachromosomal translocations. We found no evidence for large interchromosomal translocations. Overall, the data suggest that the primary processes involved in divergence of the maize and sorghum genomes were duplications (either by polyploidy or segmental duplication) and inversions or intrachromosomal translocations.     

Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences

Managed environments in the form of well watered and water stressed trials were performed to study the genetic basis of grain yield and stay green in sorghum with the objective of validating previously detected QTL. As variations in phenology and plant height may influence QTL detection for the target traits, QTL for flowering time and plant height were introduced as cofactors in QTL analyses for yield and stay green. All but one of the flowering time QTL were detected near yield and stay green QTL. Similar co-localization was observed for two plant height QTL. QTL analysis for yield, using flowering time/plant height cofactors, led to yield QTL on chromosomes 2, 3, 6, 8 and 10. For stay green, QTL on chromosomes 3, 4, 8 and 10 were not related to differences in flowering time/plant height. The physical positions for markers in QTL regions projected on the sorghum genome suggest that the previously detected plant height QTL, Sb-HT9-1, and Dw2, in addition to the maturity gene, Ma5, had a major confounding impact on the expression of yield and stay green QTL. Co-localization between an apparently novel stay green QTL and a yield QTL on chromosome 3 suggests there is potential for indirect selection based on stay green to improve drought tolerance in sorghum. Our QTL study was carried out with a moderately sized population and spanned a limited geographic range, but still the results strongly emphasize the necessity of corrections for phenology in QTL mapping for drought tolerance traits in sorghum.     

Construction of an RFLP map in sorghum and comparative mapping in maize.

An F2 population derived from a cross between Sorghum bicolor ssp. bicolor ('CK60') and Sorghum bicolor ssp. drummondii ('PI229828') was used to develop an RFLP genetic linkage map of sorghum. The map consists of 201 loci distributed among 10 linkage groups covering a map distance of 1530 cM, with an average 8 cM between adjacent loci. Maize genomic probes (52), maize cDNA probes (124), and sorghum genomic probes (10) were used to define the loci (55, 136, and 10, respectively). Ninety-five percent of the loci fit expected segregation ratios. The loci with distorted segregation ratios were confined almost exclusively to a region of one linkage group. Comparison of sorghum and maize maps indicated high correspondence between the two genomes in terms of loci order and genetic distance. Many loci linked in maize (45 of 55) were also linked in sorghum. Instances of both conserved and rearranged locus orders were detected.     

Supermodels: sorghum and maize provide mutual insight into the genetics of flowering time

Nested association mapping (NAM) offers power to dissect complex, quantitative traits. This study made use of a recently developed sorghum backcross (BC)-NAM population to dissect the genetic architecture of flowering time in sorghum; to compare the QTL identified with other genomic regions identified in previous sorghum and maize flowering time studies and to highlight the implications of our findings for plant breeding. A subset of the sorghum BC-NAM population consisting of over 1,300 individuals from 24 families was evaluated for flowering time across multiple environments. Two QTL analysis methodologies were used to identify 40 QTLs with predominately small, additive effects on flowering time; 24 of these co-located with previously identified QTL for flowering time in sorghum and 16 were novel in sorghum. Significant synteny was also detected with the QTL for flowering time detected in a comparable NAM resource recently developed for maize (Zea mays) by Buckler et al. (Science 325:714–718, 2009). The use of the sorghum BC-NAM population allowed us to catalogue allelic variants at a maximal number of QTL and understand their contribution to the flowering time phenotype and distribution across diverse germplasm. The successful demonstration of the power of the sorghum BC-NAM population is exemplified not only by correspondence of QTL previously identified in sorghum, but also by correspondence of QTL in different taxa, specifically maize in this case. The unification across taxa of the candidate genes influencing complex traits, such as flowering time can further facilitate the detailed dissection of the genetic control and causal genes.     

Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench

The productivity of sorghum is mainly determined by quantitative traits such as grain yield and stem sugar-related characteristics. Substantial crop improvement has been achieved by breeding in the last decades. Today, genetic mapping and characterization of quantitative trait loci (QTLs) is considered a valuable tool for trait enhancement. We have investigated QTL associated with the sugar components (Brix, glucose, sucrose, and total sugar content) and sugar-related agronomic traits (flowering date, plant height, stem diameter, tiller number per plant, fresh panicle weight, and estimated juice weight) in four different environments (two locations) using a population of 188 recombinant inbred lines (RILs) from a cross between grain (M71) and sweet sorghum (SS79). A genetic map with 157 AFLP, SSR, and EST-SSR markers was constructed, and several QTLs were detected using composite interval mapping (CIM). Further, additive × additive interaction and QTL × environmental interaction were estimated. CIM identified more than five additive QTLs in most traits explaining a range of 6.0–26.1% of the phenotypic variation. A total of 24 digenic epistatic locus pairs were identified in seven traits, supporting the hypothesis that QTL analysis without considering epistasis can result in biased estimates. QTLs showing multiple effects were identified, where the major QTL on SBI-06 was significantly associated with most of the traits, i.e., flowering date, plant height, Brix, sucrose, and sugar content. Four out of ten traits studied showed a significant QTL × environmental interaction. Our results are an important step toward marker-assisted selection for sugar-related traits and biofuel yield in sorghum.     

Genetic resolution and verification of quantitative trait loci for flowering and plant height with recombinant inbred lines of maize.

Recombinant inbred (RI) lines offer several advantages for detecting quantitative trait loci (QTLs), including increased precision of trait measurements, power for detection of additive effects, and resolution of linked QTLs. This study was conducted to detect and characterize QTLs in maize for flowering and plant height and to compare QTL detection in an early (F2:3) generation of the same population. One hundred and eighty-six RIs from a cross between inbred lines Mo17 and H99 were evaluated in a replicated field experiment and analyzed at 101 loci detected by restriction fragment length polymorphisms. QTLs were identified by single-factor analysis of variance. A total of 59 QTLs were detected for plant height, ear height, top height, anthesis, silk emergence, and anthesis to silk interval. Individual QTLs explained 2.2-15.4% of trait variation, and multiple models including all QTLs detected for a trait explained up to 52.5% of the phenotypic variation. Comparison of QTLs detected with 150 F2:3 lines from the same population indicated that 16 (70%) of the 23 F2:3 QTLs were also observed in the F6:7 generation. Parental effects were consistent across generations. At 14 of the 16 QTLs detected in both generations, genetic effects were smaller in the F6:7. Also, some QTLs detected in the F2:3 were resolved into multiple linked QTLs in the F6:7, indicating the additional power of RI populations for mapping, with important implications for marker-assisted selection as well as map-based cloning of QTLs. Key words : Zea mays, RFLP, plant breeding, genetics, recombination.     

Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the<Emphasis Type="Italic"> Oryza sativa</Emphasis> variety IR64 and the wild relative<Emphasis Type="Italic"> O. rufipogon</Emphasis>

A BC₂F₂ population developed from an interspecific cross between Oryza sativa (cv IR64) and O. rufipogon (IRGC 105491) was used in an advanced backcross QTL analysis to identify and introduce agronomically useful genes from this wild relative into the cultivated gene pool. The objectives of this study were: (1) to identify putative yield and yield component QTLs that can be useful to improve the elite cultivar IR64; (2) to compare the QTLs within this study with previously reported QTLs in rice as the basis for identifying QTLs that are stable across different environments and genetic backgrounds; and (3) to compare the identified QTLs with previously reported QTLs from maize to examine the degree of QTL conservation across the grass family. Two hundred eighty-five families were evaluated in two field environments in Indonesia, with two replications each, for 12 agronomic traits. A total of 165 markers consisting of 131 SSRs and 34 RFLPs were used to construct the genetic linkage map. By employing interval mapping and composite interval mapping, 42 QTLs were identified. Despite its inferior performance, 33% of the QTL alleles originating from O. rufipogon had a beneficial effect for yield and yield components in the IR64 background. Twenty-two QTLs (53.4%) were located in similar regions as previously reported rice QTLs, suggesting the existence of stable QTLs across genetic backgrounds and environments. Twenty QTLs (47.6%) were exclusively detected in this study, uncovering potentially novel alleles from the wild, some of which might improve the performance of the tropical indica variety IR64. Additionally, several QTLs for plant height, grain weight, and flowering time detected in this study corresponded to homeologous regions in maize containing previously detected maize QTLs for these traits.     

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.     

Comparative genetic mapping between duplicated segments on maize chromosomes 3 and 8 and homoeologous regions in sorghum and sugarcane

Comparative mapping within maize, sorghum and sugarcane has previously revealed the existence of syntenic regions between the crops. In the present study, mapping on the sorghum genome of a set of probes previously located on the maize and sugarcane maps allow a detailed analysis of the relationship between maize chromosomes 3 and 8 and sorghum and sugarcane homoeologous regions. Of 49 loci revealed by 46 (4 sugarcane and 42 maize) polymorphic probes in sorghum, 42 were linked and were assigned to linkage groups G (28), E (10) and I (4). On the basis of common probes, a complete co-linearity is observed between sorghum linkage group G and the two sugarcane linkage groups II and III. The comparison between the consensus sorghum/sugarcane map (G/II/III) and the maps of maize chromosomes 3 and 8 reveals a series of linkage blocks within which gene orders are conserved. These blocks are interspersed with non-homoeologous regions corresponding to the central part of the two maize chromosomes and have been reshuffled, resulting in several inversions in maize compared to sorghum and sugarcane. The results emphasize the fact that duplication will considerably complicate precise comparative mapping at the whole genome scale between maize and other Poaceae.     

Genetic analysis of drought tolerance in maize by molecular markers. II. Plant height and flowering

Drought is a serious agronomic problem, and one of the most important factors contributing to crop yield loss. In maize grown in temperate areas, drought stress occurs just before and during the flowering period; consequently, tolerance to water stress in this species is largely determined by events that occur at or shortly after flowering. The purposes of our investigation were: (1)?to identify the chromosomal regions where factors conferring drought tolerance for traits related to plant development and flowering are located and (2)?to compare these regions with those carrying QTLs controlling these traits, in order to get indirect information on the genetic and physiological basis of maize response to water stress. To this aim, we performed a linkage analysis between the expression of male and female flowering time, anthesis-silking interval (ASI), plant height and molecular markers. The experiment was carried out under two environmental conditions, well-watered and water-stressed, on a maize population of 142 recombinant inbred lines obtained by selfing the F₁ between lines B73 and H99 and genotyped by RFLP, microsatellites (SSR) and AFLP markers, for a total of 153 loci. Linkage analysis revealed that, for male flowering time and plant height, most of the QTLs detected were the same under control and stress conditions. In contrast, with respect to female flowering time and ASI diverse QTLs appeared to be expressed either under control conditions or under stress. All of the QTLs conferring tolerance to drought were located in a different chromosome position as compared to the map position of the factors controlling the trait per se. This suggests that plant tolerance, in its different components, is not attributable to the presence of favourable allelic combinations controlling the trait but is based on physiological characteristics not directly associated with the control of the character.     

Quantitative trait loci influencing drought tolerance in grain sorghum (Sorghum bicolor L. Moench)

Drought is a major constraint in sorghum production worldwide. Drought-stress in sorghum has been characterized at both pre-flowering and post-flowering stages resulting in a drastic reduction in grain yield. In the case of post-flowering drought stress, lodging further aggravates the problem resulting in total loss of crop yield in mechanized agriculture. The present study was conducted to identify quantitative trait loci (QTLs) controlling post-flowering drought tolerance (stay green), pre-flowering drought tolerance and lodging tolerance in sorghum using an F₇ recombinant inbred line (RIL) population derived from the cross SC56×Tx7000. The RIL lines, along with parents, were evaluated for the above traits in multiple environments. With the help of a restriction fragment length polymorphism (RFLP) map, which spans 1,355 cM and consists of 144 loci, nine QTLs, located over seven linkage groups were detected for stay green in several environments using the method of composite interval mapping. Comparison of the QTL locations with the published results indicated that three QTLs located on linkage groups A, G and J were consistent. This is considered significant since the stay green line SC56 used in our investigation is from a different source compared to B35 that was used in all the earlier investigations. Comparative mapping has shown that two stay green QTLs identified in this study corresponded to stay green QTL regions in maize. These genomic regions were also reported to be congruent with other drought-related agronomic and physiological traits in maize and rice, suggesting that these syntenic regions might be hosting a cluster of genes with pleiotropic effects implicated in several drought tolerance mechanisms in these grass species. In addition, three and four major QTLs responsible for lodging tolerance and pre-flowering drought tolerance, respectively, were detected. This investigation clearly revealed the important and consistent stay green QTLs in a different stay green source that can logically be targeted for positional cloning. The identification of QTLs and markers for pre-flowering drought tolerance and lodging tolerance will help plant breeders in manipulating and pyramiding those traits along with stay green to improve drought tolerance in sorghum. Received: 2 June 2000 / Accepted: 15 November 2000     

QTL mapping analysis of plant height and ear height of maize (Zea mays L.)

Genetic map containing 103 microsatellite loci obtained on 200 F2 plants derived from the cross R15 x 478 was used for quantitative trait loci (QTL) mapping in maize. QTL were characterized in a population of 200 F2:4 lines, derived from selfing the F2 plants, and were evaluated with two replications in two environments. QTL determinations were made from the mean of these two environments. Plant height (PH) and ear height (EH) were measured. Using composite interval mapping (CIM) method, a total of 14 distinct QTLs were identified: nine for PH and five for EH. Additive, partial dominance, dominance, and overdominance actions existed among all detected QTL affecting plant height and ear height. The QTL explained 78.27% of the phenotypic variance of PH and 41.50% of EH. The 14 QTLs displayed mostly dominance or partial dominance gene action and mapped to chromosomes 2, 3, 4, 8 and 9.     

Quantitative trait loci analysis of plant height and ear height in maize (Zea mays L.)

Genetic map containing 103 microsatellite loci obtained on 200 F₂ plants derived from the cross R15 × 478 was used for quantitative trait loci (QTL) mapping in maize. QTLs were characterized in a population of 200 F_2:4 lines, derived from selfing the F₂ plants, and were evaluated with two replications in two environments. QTL determinations were made from the mean of these two environments. Plant height (PH) and ear height (EH) were measured. Using composite interval mapping (CIM) method, a total of 14 distinct QTLs were identified: nine for PH and five for EH. Additive, partial dominance, dominance, and overdominance actions existed among all detected QTLs affecting plant height and ear height. The QTLs explained 78.27% of the phenotypic variance of PH and 41.50% of EH. The 14 QTLs displayed mostly dominance or partial dominance gene action and mapped to chromosomes 2, 3, 4, 8, and 9. The text was submitted by the authors in English.     

QTL identification of flowering time at three different latitudes reveals homeologous genomic regions that control flowering in soybean

Since the genetic control of flowering time is very important in photoperiod-sensitive soybean (Glycine max (L.) Merr.), genes affecting flowering under different environment conditions have been identified and described. The objectives were to identify quantitative trait loci (QTLs) for flowering time in different latitudinal and climatic regions, and to understand how chromosomal rearrangement and genome organization contribute to flowering time in soybean. Recombinant inbred lines from a cross between late-flowering ‘Jinpumkong 2’ and early-flowering ‘SS2-2’ were used to evaluate the phenotypic data for days to flowering (DF) collected from Kamphaeng Saen, Thailand (14°01′N), Suwon, Korea (37°15′N), and Longjing, China (42°46′N). A weakly positive phenotypic correlation (r = 0.36) was found between DF in Korea and Thailand; however, a strong correlation (r = 0.74) was shown between Korea and China. After 178 simple sequence repeat (SSR) markers were placed on a genetic map spanning 2,551.7 cM, four independent DF QTLs were identified on different chromosomes (Chrs). Among them, three QTLs on Chrs 9, 13 and 16 were either Thailand- or Korea-specific. The DF QTL on Chr 6 was identified in both Korea and China, suggesting it is less environment-sensitive. Comparative analysis of four DF QTL regions revealed a syntenic relationship between two QTLs on Chrs 6 and 13. All five duplicated gene pairs clustered in the homeologous genomic regions were found to be involved in the flowering. Identification and comparative analysis of multiple DF QTLs from different environments will facilitate the significant improvement in soybean breeding programs with respect to control of flowering time.     

QTL analysis of morphological traits in eggplant and implications for conservation of gene function during evolution of solanaceous species

An interspecific F(2) population from a cross between cultivated eggplant, Solanum melongena, and its wild relative, S. linnaeanum, was analyzed for quantitative trait loci (QTL) affecting leaf, flower, fruit and plant traits. A total of 58 plants were genotyped for 207 restriction fragment length polymorphism (RFLP) markers and phenotyped for 18 characters. One to eight loci were detected for each trait with a total of 63 QTL identified. Overall, 46% of the QTL had allelic effects that were the reverse of those predicted from the parental phenotypes. Wild alleles that were agronomically superior to the cultivated alleles were identified for 42% of the QTL identified for flowering time, flower and fruit number, fruit set, calyx size and fruit glossiness. Comparison of the map positions of eggplant loci with those for similar traits in tomato, potato and pepper revealed that 12 of the QTL have putative orthologs in at least one of these other species and that putative orthology was most often observed between eggplant and tomato. Traits showing potential orthology were: leaf length, shape and lobing; days to flowering; number of flowers per inflorescence; plant height and apex, leaf and stem hairiness. The functionally conserved loci included a major leaf lobing QTL ( llob6.1) that is putatively orthologous to the potato leaf ( c) and/or Petroselinum ( Pts) mutants of tomato, two flowering time QTL ( dtf1.1, dtf2.1) that also have putative counterparts in tomato and four QTL for trichomes that have potential orthologs in tomato and potato. These results support the mounting evidence of conservation of gene function during the evolution of eggplant and its relatives from their last common ancestor and indicate that this conservation was not limited to domestication traits.     

Identification of Dw1, a Regulator of Sorghum Stem Internode Length

Sorghum is an important C4 grain and grass crop used for food, feed, forage, sugar, and biofuels. In its native Africa, sorghum landraces often grow to approximately 3–4 meters in height. Following introduction into the U.S., shorter, early flowering varieties were identified and used for production of grain. Quinby and Karper identified allelic variation at four loci designated Dw1-Dw4 that regulated plant height by altering the length of stem internodes. The current study used a map-based cloning strategy to identify the gene corresponding to Dw1. Hegari (Dw1dw2Dw3dw4) and 80M (dw1dw2Dw3dw4) were crossed and F₂ and HIF derived populations used for QTL mapping. Genetic analysis identified four QTL for internode length in this population, Dw1 on SBI-09, Dw2 on SBI-06, and QTL located on SBI-01 and SBI-07. The QTL on SBI-07 was ~3 Mbp upstream of Dw3 and interacted with Dw1. Dw1 was also found to contribute to the variation in stem weight in the population. Dw1 was fine mapped to an interval of ~33 kbp using HIFs segregating only for Dw1. A polymorphism in an exon of Sobic.009G229800 created a stop codon that truncated the encoded protein in 80M (dw1). This polymorphism was not present in Hegari (Dw1) and no other polymorphisms in the delimited Dw1 locus altered coding regions. The recessive dw1 allele found in 80M was traced to Dwarf Yellow Milo, the progenitor of grain sorghum genotypes identified as dw1. Dw1 encodes a putative membrane protein of unknown function that is highly conserved in plants.     

Host plant diversity of Sesamia calamistis: cytochrome b gene sequences reveal local genetic differentiation

Sesamia calamistis Hampson (Lepidoptera: Noctuidae) is one of the indigenous stem borer pests associated with maize ( Zea mays L.) and sorghum [ Sorghum bicolor (L.) Moench] (both Poaceae) in Africa. Its pest status varies across the continent and this has been attributed to variation in diet breadth and ecological preferences among populations. Its larvae were found on 12 plant species during a study initiated at four sites (Muhaka, Mtito Andei, Kakamega, and Suam) in Kenya to estimate its diet breadth and genetic population structure. Ten of the infested plant species belonged to the family Poaceae [ Echinochloa haploclada (Stapf) Stapf, Eleusine corocana L., Eleusine jaegeri Pilg., Panicum deustum Thunb, Panicum maximum Jacquin, Pennisetum purpureum Schumacher, Setaria verticillata (L.) P. Beauv., Sorghum arundinaceum (Desvaux) Stapf, S. bicolor , and Z. mays ]; the other two were Cyperaceae: Cyperus distans L. and Cyperus dives Delile. Combined with collections from other African countries (Uganda, South Africa, Benin, Ghana, Nigeria, and Togo), comparisons of partial cytochrome b sequences revealed the presence of 68 haplotypes that differentiated into clades I and II. In Kenya, the two clades colonized different regions, except in Mtito Andei where they co-existed. Individuals from Mtito Andei could be separated based on their host plants: clade I with 14 haplotypes was found mainly on maize (78.6%), whereas clade II with 10 haplotypes was found mainly among wild host plants (63.6%). Detection of divergence among these clades with cytochrome b suggests that their evolutionary separation may have taken place about one million years ago. This article discusses the potential implication of this differentiation for the management of S .  calamistis as a pest of maize and sorghum in Africa.