Search

Key messageSeven novel alleles ofSBEIIband one allele ofSSIIaco-segregated with the ASV phenotype and contributed to distinct starch quality traits important for food-processing applications.AbstractSorghum is an important food crop for millions of people in Africa and Asia. Whole-genome re-sequencing of sorghum EMS mutants exhibiting an alkali spreading value (ASV) phenotype revealed candidate SNPs inSobic.004G163700andSobic.010G093400. Comparative genomics identifiedSobic.010G093400as astarch synthase IIaandSobic.004G163700as astarch branching enzyme IIb. Segregation analyses showed that mutations inSobic.010G093400orSobic.004G163700co-segregated with the ASV phenotype. Mutants inSSIIaexhibited no change in amylose content but expressed lower final viscosity and lower starch gelatinization temperature (GT) than starches from non-mutant plants. ThesbeIIbmutants exhibited significantly higher amylose levels and starch GT and lower viscosity compared to non-mutant starches andssIIamutants. Mutations inSBEIIbhad a dosage-dependent effect on amylose content. Double mutants ofsbeIIbandssIIaresembled theirsbeIIbparent in amylose content, starch thermal properties and viscosity profiles. These variants will provide opportunities to produce sorghum varieties with modified starch end-use qualities important for the beer brewing and baking industries and specialty foods for humans with diabetes.

The eastern Africa region, Ethiopia and its surroundings, is considered as the center of origin and diversity for sorghum, and has contributed to global sorghum genetic improvement. The germplasm from this region harbors enormous genetic variation for various traits but little is known regarding the genetic architecture of most traits. Here, 1425 Ethiopian landrace accessions were phenotyped under field conditions for presence or absence of awns, panicle compactness and shape, panicle exsertion, pericarp color, glume cover, plant height and smut resistance under diverse environmental conditions in Ethiopia. In addition, F1 hybrids obtained from a subset of 1341 accessions crossed to an A1 cytoplasmic male sterile line, ATx623, were scored for fertility/sterility reactions. Subsequently, genotyping-by-sequencing generated a total of 879,407 SNPs from which 72,190 robust SNP markers were selected after stringent quality control (QC). Pairwise distance-based hierarchical clustering identified 11 distinct groups. Of the genotypes assigned to either one of the 11 sub-populations, 65% had high ancestry membership coefficient with the likelihood of more than 0.60 and the remaining 35% represented highly admixed accessions. A genome-wide association study (GWAS) identified loci and SNPs associated with aforementioned traits. GWAS based on compressed mixed linear model (CMLM) identified SNPs with significant association (FDR ≤ 0.05) to the different traits studied. The percentage of total phenotypic variation explained with significant SNPs across traits ranged from 2 to 43%. Candidate genes showing significant association with different traits were identified. The sorghum bHLH transcription factor, ABORTED MICROSPORES was identified as a strong candidate gene conditioning male fertility. Notably, sorghum CLAVATA1 receptor like kinase, known for regulation of plant growth, and the ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR gene RAP2-7, known to suppress transition to flowering, were significantly associated with plant height. In addition, the YELLOW SEED1 like MYB transcription factor and TANNIN1 showed strong association with pericarp color validating previous observations. Overall, the genetic architecture of natural variation representing the complex Ethiopian sorghum germplasm was established. The study contributes to the characterization of genes and alleles controlling agronomic traits, and will serve as a source of markers for molecular breeding.

Genetic analysis of brown midrib sorghum (Sorghum bicolor) mutant lines assembled in our program has previously shown that the mutations fall into four allelic groups, bmr2, bmr6, bmr12 or bmr19. Causal genes for allelic groups bmr2, bmr6 and bmr12, have since been identified. In this report, we provide evidence for the nature of the bmr19 mutation. This was accomplished by introgressing each of the four bmr alleles into nine different genetic backgrounds. Polymorphisms from four resequenced bulks of sorghum introgression lines containing either mutation, relative to those of a resequenced bulk of the nine normal midrib recurrent parent lines, were used to locate their respective causal mutations. The analysis confirmed the previously reported causal mutations for bmr2 and bmr6 but failed in the case of bmr12-bulk due to a mixture of mutant alleles at the locus among members of that mutant bulk. In the bmr19-bulk, a common G → A mutation was found among all members in Sobic.001G535500. This gene encodes a putative folylpolyglutamate synthase with high homology to maize Bm4. The brown midrib phenotype co-segregated with this point mutation in two separate F2 populations. Furthermore, an additional variant allele at this locus obtained from a TILLING population also showed a brown midrib phenotype, confirming this locus as Bmr19.

Stalk rots are important biotic constraints to sorghum production worldwide. Several pathogens may be associated with the disease, but Macrophomina phaseolina and Fusarium thapsinum are recognized as the major causal organisms. The diseases become more aggressive when drought and high-temperature stress occur during grain filling. Progress in genetic improvement efforts has been slow due to lack of effective phenotyping protocol and the strong environmental effect on disease incidence and severity. Deployment of modern molecular tools is expected to accelerate efforts to develop resistant hybrids. This study was aimed at identifying genomic regions associated with resistance to both causal organisms. A sorghum diversity panel consisting of 300 genotypes assembled from different parts of the world was evaluated for response to infection by both pathogens. Community resources of 79,132 single nucleotide polymorphic (SNP) markers developed on the panel were used in association studies using a multi-locus mixed model to map loci associated with stalk rot resistance. Adequate genetic variation was observed for resistance to both pathogens. Structure analysis grouped the genotypes into five subpopulations primarily based on the racial category of the genotypes. Fourteen loci and a set of candidate genes appear to be involved in connected functions controlling plant defense response. However, each associated SNP had relatively small effect on the traits, accounting for 19–30% of phenotypic variation. Linkage disequilibrium analyses suggest that significant SNPs are genetically independent. Estimation of frequencies of associated alleles revealed that durra and caudatum subpopulations were enriched for resistant alleles, but the results suggest complex molecular mechanisms underlying resistance to both pathogens.

The ease with which seeds are detached from panicles is one of the early domestication traits. Genotypes with sticky panicles are hard to thresh, and whenever threshed, the grain tends to remain attached to the glume which reduces market value and processability. This study was conducted to determine the genetic mechanisms underlying the threshability trait in sorghum. Four seed parents and eleven pollinators differing for threshability were intercrossed in Design II mating scheme and the resulting hybrids and the parents were grown in four environments. Threshability was estimated as the ratio of seed yield to panicle weight (TW) and proportion of seeds without sticky glumes (TG). Variation was significant among the entries, inbreds and hybrids with GCA for TG and TW varying markedly. Mean TG for inbred and hybrids of low threshable genotypes was not markedly different indicating that threshability trait is under the control of additive genes with dominant or partially dominant effects. Segregation analysis indicates that the TG trait may be under the control of few major genes with approximately one to three loci affecting the trait.

The Existence and Distribution of Jatropha curcas L. germplasms in the Northwest zone of Nigeria is hereby reported with coordinates and point mapping. Fifty seven (57) accessions were collected from the seven States of the zone which spans across the Sahel, Sudan and Guinea Savannas. The collection was made from 18th to 22nd of August 2009. A plantation was established from these collections and the seeds from 39 different provenances of the seven States were analyzed for their oil content. The mean oil content ranged from 20.29% to 61.83% (CV 29.11%). The 100-seed weight ranged from 28.558g to 80.046g. There was a positive correlation between 100 seed weight and oil content (r = 0.235). The accessions from Kaduna State, spanning through the Sudan and Northern Guinea Savanna, had the highest mean oil content followed by those from Kano and Katsina States in the Sudan Savanna ecology. There were no significant differences (p < 0.5) in the accessions from Jigawa, Kebbi, Sokoto and Zamfara States which are mainly located in the Sudano-Sahelian Savanna agro-ecological zone. Most of the provenances visited were more than 50 yrs old as reported by the locals, implying that Jatropha has been a long existing crop in Nigeria. The existence of Jatropha in almost all the visited locations, and the impressive intensity of fruiting as sighted on the trees and their oil contents show that the potential for adopting it into the farming systems of these localities as source of renewable energy exists. (C) 2011 Elsevier Ltd. All rights reserved.

Genetics of harvest index and leaf-yield index in cowpea (Vigna unguiculata [L.] Walp) were studied via generation mean analysis to understand the gene action controlling the two traits and to identify the most appropriate breeding strategies for improving these traits. Three cultivars involving IAR-00-1074 with good fodder yield and IT93K-499-35 and IT93K-452-1 with high grain yield were used during 2005 at the Institute for Agricultural Research (IAR), Samaru, Nigeria. The parents, their F1, F2 and two backcross generations were evaluated using a randomized complete-block design. Highly significant differences were observed among the five generations for harvest index and leaf-yield index. F1 means were closer to the parent with higher harvest index for both crosses. This suggested that dominance was involved in expression of harvest index. The same trend was observed for leaf-yield index. Backcrossing to both parents showed good convergence of genes on the recurrent parent in the cross IAR-00-1074 × IT...