Gebisa Ejeta

Heterogeneous inbred family (HIF) analysis: a method for developing near-isogenic lines that differ at quantitative trait loci

Abtract Analysis of near-isogenic lines (NILs) that differ at quantitative trait loci (QTL) can be an effective approach for the detailed mapping and characterization of individual loci. Although NILs are useful for genetic and physiological studies, the time and effort required to develop these lines have limited their use. Here we describe a procedure to identify NILs for any region of the genome that can be analyzed with molecular or other genetic markers. The procedure utilizes molecular markers to identify heterogeneous inbred families (HIFs) that segregate for a genomic region of interest. Each HIF is isogenic at the majority of loci in the genome, but NILs differing for markers linked to QTL of interest can be extracted from segregating families. The application of this procedure is described for two QTL associated with seed weight in sorghum. A population of 98 HIFs was screened with two RAPD markers from different linkage groups that were associated with seed weight. Three segregating families were identified for each marker. The progeny of these HIFs were characterized for the segregation of seed weight and other yield components and for markers flanking each QTL. NILs derived from each HIF had significantly different seed weights confirming the presence of at least two loci that influence seed weight in sorghum.

Genetic analysis of post-flowering drought tolerance and components of grain development in Sorghum bicolor (L.) Moench

Drought is a serious agronomic problem and the single greatest factor contributing to crop yield loss in the world today. This problem may be alleviated by developing crops that are well adapted to dry-land environments. Sorghum (Sorghum bicolor (L.) Moench) is one of the most drought-tolerant grain crops and is an excellent crop model for evaluating mechanisms of drought tolerance. In this study, a set of 98 recombinant inbred (RI) sorghum lines was developed from a cross between two genotypes with contrasting drought reactions, TX7078 (pre-flowering-tolerant, post-flowering susceptible) and B35 (pre-flowering susceptible, post-flowering-tolerant). The RI population was characterized under drought and non-drought conditions for the inheritance of traits associated with post-flowering drought tolerance and for potentially related components of grain development. Quantitative trait loci (QTL) analysis identified 13 regions of the genome associated with one or more measures of post-flowering drought tolerance. Two QTL were identified with major effects on yield and staygreen’ under post-flowering drought. These loci were also associated with yield under fully irrigated conditions suggesting that these tolerance loci have pleiotropic effects on yield under non-drought conditions. Loci associated with rate and/or duration of grain development were also identified. QTL analysis indicated many loci that were associated with both rate and duration of grain development. High rate and short duration of grain development were generally associated with larger seed size, but only two of these loci were associated with differences in stability of performance under drought.

Selecting sorghum genotypes expressing a quantitative biosynthetic trait that confers resistance to Striga

Abstract One of the best characterized mechanisms of host resistance to witchweeds ( Striga spp.) is exudation by host plant roots of relatively low amounts of compounds that Striga seeds require as stimulants for germination. We find that all sorghums tested, regardless of whether they are susceptible or resistant to Striga , produce equivalent amounts of sorgoleone, the alkylated hydroquinone we previously identified from sorghum root exudate as the first host-derived Striga germination stimulant to be characterized. In contrast, some highly resistant sorghums produce relatively tiny amounts of another germination stimulant, as yet unidentified but with properties quite different from sorgoleone, whereas all susceptible sorghums produce relatively large amounts. A simple, rapid and nondestructive agar gel assay which detects this second stimulant, but not sorgoleone, reliably distinguishes low ( Striga resistant) and high ( Striga susceptible) stimulating parental genotypes and progenies from crosses among them. Because the lack of a reliable and rapid method for screening germplasm and breeding progenies has hampered the development of crop varieties resistant to Striga , this gel assay is expected to greatly enhance the efficiency of sorghum breeding for Striga resistance.

A Genomewide Analysis of the Cinnamyl Alcohol Dehydrogenase Family in Sorghum [Sorghum bicolor (L.) Moench] Identifies SbCAD2 as the Brown midrib6 Gene

The content and composition of the plant cell wall polymer lignin affect plant fitness, carbon sequestration potential, and agro-industrial processing. These characteristics, are heavily influenced by the supply of hydroxycinnamyl alcohol precursors synthesized by the enzyme cinnamyl alcohol dehydrogenase (CAD). In angiosperms, CAD is encoded by a multigene family consisting of members thought to have distinct roles in different stages of plant development. Due to the high sequence similarity among CAD genes, it has been challenging to identify and study the role of the individual genes without a genome sequence. Analysis of the recently released sorghum genome revealed the existence of 14 CAD-like genes at seven genomic locations. Comparisons with maize and rice revealed subtle differences in gene number, arrangement, and expression patterns. Sorghum CAD2 is the predominant CAD involved in lignification based on the phylogenetic relationship with CADs from other species and genetic evidence showing that a set of three allelic brown midrib (bmr) lignin mutants contained mutations in this gene. The impact of the mutations on the structure of the protein was assessed using molecular modeling based on X-ray crystallography data of the closely related Arabidopsis CAD5. The modeling revealed unique changes in structure consistent with the observed phenotypes of the mutants.

Allelic association, chemical characterization and saccharification properties of brown midrib mutants of sorghum (Sorghum bicolor (L.) Moench).

Genetic improvement of biomass crops can significantly reduce the overall cost of biomass-to-ethanol conversion. The conversion of cellulose to monomeric sugar units is affected by lignin content and composition. Sorghum has attracted the attention of the scientific and industrial community as a promising source of biomass for bioenergy due to its great yield potential and tolerance to stresses. The brown midrib (bmr) mutants of sorghum are characterized by brown vascular tissue associated with altered lignin content. Twenty-eight bmr mutants have been identified since the late 1970s, but the allelic relationships have not been fully established, and the function of only one of the Bmr loci has been unequivocally established. In this study, we combined genetic and chemical approaches to establish that there are mutations at least four independent bmr loci, represented by the bmr2, bmr6, bmr12 and bmr19 groups. Since each allelic group presents unique staining characteristics, rapid classification of emerging bmr lines into the existing groups can be achieved using phloroglucinol-HCl as a histochemical stain. In addition, pyrolysis-gas chromatography-mass spectrometry, enabled the characterization of changes in subunit lignin composition in each of the allelic groups, to help predict the genes underlying the mutations. Enzymatic saccharification of stover from plants representing each allelic bmr group demonstrated that lignin changes in lines belonging to the bmr2, bmr6 and bmr12 groups can increase glucose yields, up to 25% compared to wild-type isolines. In order to expedite the selection of the bmr mutant alleles in breeding populations, we have developed molecular markers specific for bmr7 and bmr25, two novel mutant alleles of the gene encoding caffeic acid O-methyl transferase. Based on the results from this study, we propose to rename the bmr mutants in a manner that reflects the number of independent loci.

QTL analysis of early-season cold tolerance in sorghum

Cool temperatures during the early-growing season are a major limitation to growing sorghum [Sorghum bicolor (L.) Moench] in temperate areas. Several landraces from China have been found to exhibit higher emergence and greater seedling vigor under cool conditions than most breeding lines currently available, but tend to lack desirable agronomic characteristics. The introgression of desirable genes from Chinese landraces into elite lines could be expedited by marker-assisted selection. Using a population of 153 RI lines, developed from a cross between Chinese landrace ‘Shan Qui Red,’ (SQR, cold-tolerant) and SRN39 (cold-sensitive), QTL associated with early-season performance under both cold and optimal conditions were identified by single marker analysis, simple interval mapping (SIM), and composite interval mapping (CIM). Germination was observed under controlled conditions, and other traits were measured in field plantings. Two QTL for germination were identified: one on linkage group SBI-03a, derived from SRN39, was significant under cold and optimal temperatures. The other, on group SBI-07b, showed greater significance under cold temperatures and was contributed by SQR. A region of group SBI-01a, derived from SQR, showed strong associations with seedling emergence and seedling vigor scores under early and late field plantings. A QTL for both early and late emergence was identified by CIM on SBI-02 which favored the SRN39 allele. SIM identified a QTL for early vigor on SBI-04 favoring the SQR genotype. Further studies are needed to validate the effects of these QTL, but they represent the first step in development of a marker-assisted breeding effort to improve early-season performance in sorghum.

Resistance to Striga hermonthica in a maize inbred line derived from Zea diploperennis.

Breeding for resistance to Striga in maize (Zea mays), with paucity of donor source and known mechanisms of resistance, has been challenging. Here, post-attachment development of S. hermonthica was monitored on two maize inbreds selected for field resistance and susceptibility reactions to Striga at the International Institute of Tropical Agriculture. Haustorial invasion of the parasite into roots of these inbreds was examined histologically. Morphological differences were observed between roots of the susceptible and the resistant inbreds. The resistant maize had fewer Striga attachments, delayed parasitic development and higher mortality of attached parasites compared with the susceptible inbred. Striga on the susceptible inbred usually penetrated the xylem and showed substantial internal haustorial development. Haustorial ingress on the resistant inbred was often stopped at the endodermis. Parasites able to reach resistant host xylem vessels showed diminished haustorial development relative to those invading susceptible roots. These results suggest that the resistant inbred expresses a developmental barrier and incompatible response against Striga parasitism.

Marker-Assisted Selection in Sorghum

Sorghum [Sorghum bicolor (L.) Moench] is an important food and feed crop in many parts of the world, and has potential uses in the biofuels industry. Compared to most other cereals, sorghum is more tolerant to many abiotic stresses, including heat, drought, and flooding, making it an ideal crop for growing on marginal lands as demands for food, feed, and energy increase. Though it is generally stress-tolerant, the true potential of sorghum can only be realized through concerted genetic improvement programs. The use of DNA-based markers for the genetic analysis and manipulation of important agronomic and stress-tolerance traits is becoming an increasingly useful tool in sorghum improvement. The known germplasm of sorghum is incredibly diverse, and molecular markers are being used to assess this diversity to help manage large germplasm collections, and to make these collections more useful to breeders. Molecular markers have been used in sorghum to identify quantitative trait loci (QTL) for many complex traits, including pre-flowering and post-flowering drought tolerance, early-season cold tolerance, and resistance to the parasitic weed Striga. However, progress in utilizing these QTL had been limited by the lack of a standard genetic map and a common nomenclature for the various linkage groups of sorghum. Fortunately, the genetic map of sorghum has recently become standardized, and has also been linked to physical chromosomes. The use of a common map will facilitate the exchange of marker and QTL information between sorghum research groups. This will allow independent validation of QTL and should expedite efforts to use these QTL for the development of improved sorghum cultivars through marker-assisted selection and trait introgression. Newer, faster marker technologies based on single nucleotide polymorphisms (SNPs), and mapping methods based on linkage disequilibrium (association mapping), will soon become useful tools for future efforts to improve this important crop.

Towards effective resistance to Striga in African maize

The fascinating biology of Striga parasitism is manifest through a series of signal exchanges between the parasite and its host. As an obligate root hemi-parasite, Striga development is cued to exudates and solutes of host roots but with negative ramifications on host plant health. Striga control in crops, via a variety of biotechnological approaches, needs to be based on increased understanding of this intricate biology. Maize has become the major cereal crop of Africa. However, this New World transplant has shown a paucity of Striga resistance characters relative to native sorghum. In this paper, we review growing evidence for maize genetic defenses against early pre-emergent phases of the Striga life cycle, when the tolls of parasitism are first manifest. Resistance characters first described in maize wild relatives have now been captured in Zea mays. The possible stacking of new and complementary sources of resistance in improved maize varieties targeted for Striga prone areas is discussed. An integrated approach combining genetic with other control measures is advocated with a more realistic view of the resource challenges prevalent in African agriculture.

A Novel Modified Endosperm Texture in a Mutant High-Protein Digestibility/High-Lysine Grain Sorghum (Sorghum bicolor (L.) Moench)

ABSTRACT Development of high-protein digestibility (HPD)/high-lysine (hl) sorghum mutant germplasm with good grain quality (i.e., hard endosperm texture) has been a major research objective at Purdue University. Progress toward achieving this objective, however, has been slow due to challenges posed by a combination of genetic and environmental factors. In this article, we report on the identification of a sorghum grain phenotype with a unique modified endosperm texture that has near-normal hardness and possesses superior nutritional quality traits of high digestibility and enhanced lysine content. These modified endosperm lines were identified among F6 families developed from crosses between hard endosperm, normal nutritional quality sorghum lines, and improved HPD/hl sorghum mutant P721Q-derived lines. A novel vitreous endosperm formation originated in the central portion of the kernel endosperm with opaque portions appearing both centrally and peripherally surrounding the vitreous portion. Kernels exhi...