Haplotypes at the sorghum ARG4 and ARG5 NLR loci confer resistance to anthracnose

Sorghum anthracnose caused by the fungus Colletotrichum sublineola (Cs) is a damaging disease of the crop. Here, we describe the identification of ANTHRACNOSE RESISTANCE GENES (ARG4 and ARG5) encoding canonical nucleotide-binding leucine-rich repeat (NLR) receptors. ARG4 and ARG5 are dominant resistance genes identified in the sorghum lines SAP135 and P9830, respectively, that show broad-spectrum resistance to Cs. Independent genetic studies using populations generated by crossing SAP135 and P9830 with TAM428, fine mapping using molecular markers, comparative genomics and gene expression studies determined that ARG4 and ARG5 are resistance genes against Cs strains. Interestingly, ARG4 and ARG5 are both located within clusters of duplicate NLR genes at linked loci separated by ~1 Mb genomic region. SAP135 and P9830 each carry only one of the ARG genes while having the recessive allele at the second locus. Only two copies of the ARG5 candidate genes were present in the resistant P9830 line while five non-functional copies were identified in the susceptible line. The resistant parents and their recombinant inbred lines carrying either ARG4 or ARG5 are resistant to strains Csgl1 and Csgrg suggesting that these genes have overlapping specificities. The role of ARG4 and ARG5 in resistance was validated through sorghum lines carrying independent recessive alleles that show increased susceptibility. ARG4 and ARG5 are located within complex loci displaying interesting haplotype structures and copy number variation that may have resulted from duplication. Overall, the identification of anthracnose resistance genes with unique haplotype stucture provides a foundation for genetic studies and resistance breeding.

Broad-spectrum fungal resistance in sorghum is conferred through the complex regulation of an immune receptor gene embedded in a natural antisense transcript

Sorghum (Sorghum bicolor), the fifth most widely grown cereal crop globally, provides food security for millions of people. Anthracnose caused by the fungus Colletotrichum sublineola is a major disease of sorghum worldwide. We discovered a major fungal resistance locus in sorghum composed of the nucleotide-binding leucine-rich repeat receptor gene ANTHRACNOSE RESISTANCE GENE1 (ARG1) that is completely nested in an intron of a cis-natural antisense transcript (NAT) gene designated CARRIER OF ARG1 (CARG). Susceptible genotypes express CARG and two alternatively spliced ARG1 transcripts encoding truncated proteins lacking the leucine-rich repeat domains. In resistant genotypes, elevated expression of an intact allele of ARG1, attributed to the loss of CARG transcription and the presence of miniature inverted-repeat transposable element sequences, resulted in broad-spectrum resistance to fungal pathogens with distinct virulence strategies. Increased ARG1 expression in resistant genotypes is also associated with higher histone H3K4 and H3K36 methylation. In susceptible genotypes, lower ARG1 expression is associated with reduced H3K4 and H3K36 methylation and increased expression of NATs of CARG. The repressive chromatin state associated with H3K9me2 is low in CARG-expressing genotypes within the CARG exon and higher in genotypes with low CARG expression. Thus, ARG1 is regulated by multiple mechanisms and confers broad-spectrum, strong resistance to fungal pathogens.

Physio-morphological, biochemical, and anatomical traits of drought-tolerant and susceptible sorghum cultivars under pre- and post-anthesis drought

Understanding the physiological mechanisms that control drought tolerance in crop plants is vital for effective breeding. In this study, we characterized drought stress responses in four sorghum cultivars exhibiting differential levels of drought tolerance at pre- and post-anthesis. Greenhouse-grown plants were subjected to two types of drought treatment, water stress (WS) and desiccant-induced water stress (DA), timed to occur at pre- and post-anthesis. Multiple physiological measurements were then made revealing varying responses among the experimental cultivars. The pre- and post-flowering drought-tolerant cultivar P898012 showed a significantly higher net photosynthetic rate, higher transpiration rate, and greater stomatal conductance compared to the drought-susceptible cultivars at both pre- and post-anthesis. A significantly greater stomatal size was also detected in P898012, while the highest stomatal density was found in the drought-susceptible cultivar P721Q. Meanwhile, the two post-flowering drought-tolerant cultivars P898082 and B35 had a higher starch content and exhibited greater osmotic potential under post-anthesis water stress. Compared to WS and well-watered control plants, a greater increase in root biomass was observed in P898012 under DA at pre-anthesis. This finding suggests that plants invested more assimilates into the roots under severe DA at pre-anthesis. Overall, our results show good conformity between drought tolerance in sorghum and key physiological mechanisms of stomatal conductance, root growth patterns, and starch accumulation, all of which act as coping mechanisms during critical drought-sensitive growth stages.

Genome-wide association analysis reveals seed protein loci as determinants of variations in grain mold resistance in sorghum

GWAS analysis revealed variations at loci harboring seed storage, late embryogenesis abundant protein, and a tannin biosynthesis gene associated with sorghum grain mold resistance. Grain mold is the most important disease of sorghum [Sorghum bicolor (L.) Moench]. It starts at the early stages of grain development due to concurrent infection by multiple fungal species. The genetic architecture of resistance to grain mold is poorly understood. Using a diverse set of 635 Ethiopian sorghum accessions, we conducted a multi-stage disease rating for resistance to grain mold under natural infestation in the field. Through genome-wide association analyses with 173,666 SNPs and multiple models, two novel loci were identified that were consistently associated with grain mold resistance across environments. Sequence variation at new loci containing sorghum KAFIRIN gene encoding a seed storage protein affecting seed texture and LATE EMBRYOGENESIS ABUNDANT 3 (LEA3) gene encoding a protein that accumulates in seeds, previously implicated in stress tolerance, were significantly associated with grain mold resistance. The KAFIRIN and LEA3 loci were also significant factors in grain mold resistance in accessions with non-pigmented grains. Moreover, we consistently detected the known SNP (S4_62316425) in TAN1 gene, a regulator of tannin accumulation in sorghum grain to be significantly associated with grain mold resistance. Identification of loci associated with new mechanisms of resistance provides fresh insight into genetic control of the trait, while the highly resistant accessions can serve as sources of resistance genes for breeding. Overall, our association data suggest the critical role of loci harboring seed protein genes and implicate grain chemical and physical properties in sorghum grain mold resistance.

A comprehensive phenotypic and genomic characterization of Ethiopian sorghum germplasm defines core collection and reveals rich genetic potential in adaptive traits

Understanding population genetic structure and diversity of a crop is essential in designing selection strategies in plant breeding. About 2010 Ethiopian sorghum accessions were phenotyped for different traits at multiple locations. A subset of the collection, 1628 accessions, predominantly landraces, some improved varieties, and inbred lines were genotyped by sequencing. Phenotypic data revealed association of important traits with different sorghum growing agro-climatic regions, high genetic diversity and the presence of rare natural variation in the Ethiopian sorghum germplasm. Subsequent genotypic analysis determined optimum number of sub-populations, distinct cluster groups and ancestries of each sorghum accessions. To improve utilization of germplasm, a core subset of 387 lines were selected following posteriori grouping of genotypes based on cluster groups obtained through GBS analysis followed by stratified random sampling using quantitative traits. In order to evaluate how well this new sorghum and millet innovation lab (SMIL) collection from Ethiopia is represented within the largest world sorghum collection at United States Department of Agriculture - National Plant Germplasm System (USDA-NPGS) and the sorghum association panel (SAP), comparisons were conducted based on SNP data. The SMIL collection displayed high genetic diversity with some redundancy with the USDA-NPGS germplasm but SAP showed clear distinction. Furthermore, genome-environment association analysis identified candidate genes associated with adaptation to abiotic factors, that will be important for exploitation of adaptive potential to different environments. In summary, our results described the diversity and relationship of sorghum collections, representativeness of developed core and provide novel insights into candidate genes associated to abiotic stress tolerance.

What factors are associated with maternal undernutrition in eastern zone of Tigray, Ethiopia? Evidence for nutritional well-being of lactating mothers

Background

Maternal undernutrition is a pervasive health problem among Ethiopian mothers. This study aims at identifying the level of maternal undernutrition and its associated factors in Kilte Awaleo-Health and Demographic Surveillance Site (KA-HDSS), Tigray region, Ethiopia.

Methods

Nutritional status of 2260 lactating mothers was evaluated using the mid-upper-arm circumference (MUAC). Data from the vital events and verbal autopsy databases were linked to the survey and baseline recensus data to investigate the association of adult mortality from chronic causes of death (CoD) on maternal undernutrition. We employed a generalized log-binomial model to estimate the independent effects of the fitted covariates.

Results

The overall prevalence of maternal undernutrition based on MUAC < 23 cm was 38% (95% CI: 36.1, 40.1%). Recent occurrence of household morbidity (adjusted prevalence ratio (adjPR) = 1.49; 95%CI: 1.22, 1.81) was associated with increased risk of maternal undernutrition. In addition, there was a 28% higher risk (adjPR = 1.28; 95%CI: 0.98, 1.67) of maternal undernutrition for those mothers who lived in households with history of adult mortality from chronic diseases. Especially, its association with severe maternal undernutrition was strong (adjusted OR = 3.27; 95%CI: 1.48, 7.22). In contrast, good maternal health-seeking practice (adjPR = 0.86; 95%CI: 0.77, 0.96) and production of diverse food crops (adjPR = 0.72; 95%CI: 0.64, 0.81) were associated with a lower risk of maternal undernutrition. Relative to mothers with low scores of housing and environmental factors index (HAEFI), those with medium and higher scores of HAEFI had 0.81 (adjPR = 0.81; 95%CI: 0.69, 0.95) and 0.82 (adjPR = 0.82; 95%CI: 0.72, 0.95) times lower risk of maternal undernutrition, respectively.

Conclusions

Efforts to ameliorate maternal undernutrition need to consider the influence of the rising epidemiology of adult mortality from chronic diseases. Our data clearly indicate the need for channeling the integrated intervention power of nutrition-sensitive development programs with that of nutrition-specific sectoral services.

Biomass and Bioenergy Potential of Brown Midrib Sweet Sorghum Germplasm

Public appetite for fossil fuels continues to drive energy prices and foment the build-up of intractable environmental problems. Ethanol (ETOH) production from lignocellulosic biomass grown in marginal lands offers a sustainable alternative without diverting arable land from food and feed production. The quantity and quality of lignocellulosic biomass can be enhanced by the abundant genetic diversity for biomass production as well as stem sugar and lignin composition in sorghum (Sorghum bicolor L. Moench). The objective of this study was to assess yield and quality of lignocellulosic biomass enhancement for ethanol production potential in a population of sorghum derived from two cultivars with contrasting biomass yield and compositional traits. We tested 236 recombinant inbred lines (RIL) of sorghum in a randomized complete block design (RCBD) with two replications for lignocellulosic biomass performance and determined hemicellulose, cellulose and lignin concentrations through detergent fiber analysis (DFA). The stover compositional values were used to estimate theoretical ethanol yield (ETOH on a mass basis) and production (ETOH on an area basis). Results showed that RIL carrying the brown midrib mutation had significantly higher theoretical glucose recovery (released glucose from cellulose, > 200 g kg^-1). Those carrying both mutations, had high theoretical ethanol yield (>400 L ton^-1) and high theoretical ethanol production (>14,500 L ha^-1). Lignin concentration was determined as most reliable predictor (R² = 0.67) for glucose recovery. Lignin and stem sugar concentrations (R² = 0.46 and 0.35, respectively) were good predictors for ethanol yield. Stover yield traits (R² = 0.89) were most important determinants for ethanol production. Our findings suggest that careful breeding of sorghum for genetic enhancement of biomass quantity and quality could double lignocellulosic ethanol yields.

A Large-Scale Genome-Wide Association Analyses of Ethiopian Sorghum Landrace Collection Reveal Loci Associated With Important Traits

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.

Nutrition-specific and sensitive drivers of poor child nutrition in Kilte Awlaelo-Health and Demographic Surveillance Site, Tigray, Northern Ethiopia: implications for public health nutrition in resource-poor settings

Background: Child undernutrition is a prevalent health problem and poses various short and long-term consequences. Objective: This study seeks to investigate the burden of child undernutrition and its drivers in Kilte Awlaelo-Health and Demographic Surveillance Site, Tigray, northern Ethiopia. Methods: In 2015, cross-sectional data were collected from 1,525 children aged 6-23 months. Maternal and child nutritional status was assessed using the mid upper arm circumference. Child's dietary diversity score was calculated using 24-hours dietary recall method. Log-binomial regression and partial proportional odds model were fitted to examine the drivers of poor child nutrition and child dietary diversity (CDD), respectively. Results: The burden of undernutrition and inadequate CDD was 13.7% (95% CI: 12.1-15.5%) and 81.3% (95%CI: 79.2-83.1%), respectively. Maternal undernutrition (adjusted prevalence ratio, adjPR = 1.47; 95%CI: 1.14-1.89), low CDD (adjPR = 1.90; 95%CI: 1.22-2.97), and morbidity (adjPR = 1.83; 95%CI: 1.15-2.92) were the nutrition-specific drivers of child undernutrition. The nutrition-sensitive drivers were poverty (compared to the poorest, adjPR poor = 0.65 [95%CI:0.45-0.93], adjPR medium = 0.64 [95%CI: 0.44-0.93], adjPR wealthy = 0.46 [95%CI: 0.30-0.70], and adjPR wealthiest = 0.53 [95%CI: 0.34-0.82]), larger family size (adjPR = 1.10; 95%CI: 1.02-1.18), household head's employment insecurity (adjPR = 2.10; 95%CI: 1.43-3.09), and residing in highlands (adjPR = 1.93; 95%CI: 1.36-2.75). The data show that higher CDD was positively associated with wealth (OR wealthy = 3.06 [95%CI: 1.88-4.99], OR wealthiest = 2.57 [95%CI: 1.53-4.31]), but it was inversely associated with lack of diverse food crops production in highlands (OR = 0.23; 95%CI: 0.10-0.57]). Conclusions: Our findings suggest that the burden of poor child nutrition is very high in the study area. Multi-sectoral collaboration and cross-disciplinary interventions between agriculture, nutrition and health sectors are recommended to address child undernutrition in resource poor and food insecure rural communities of similar settings.

Social determinants of adult mortality from non-communicable diseases in northern Ethiopia, 2009-2015: Evidence from health and demographic surveillance site

INTRODUCTION

In developing countries, mortality and disability from non-communicable diseases (NCDs) is rising considerably. The effect of social determinants of NCDs-attributed mortality, from the context of developing countries, is poorly understood. This study examines the burden and socio-economic determinants of adult mortality attributed to NCDs in eastern Tigray, Ethiopia.

METHODS

We followed 45,982 adults implementing a community based dynamic cohort design recording mortality events from September 2009 to April 2015. A physician review based Verbal autopsy was used to identify the most probable causes of death. Multivariable Cox proportional hazards regression was performed to identify social determinants of NCD mortality.

RESULTS

Across the 193,758.7 person-years, we recorded 1,091 adult deaths. Compared to communicable diseases, NCDs accounted for a slightly higher proportion of adult deaths; 33% vs 34.5% respectively. The incidence density rate (IDR) of NCD attributed mortality was 194.1 deaths (IDR = 194.1; 95% CI = 175.4, 214.7) per 100,000 person-years. One hundred fifty-seven (41.8%), 68 (18.1%) and 34 (9%) of the 376 NCD deaths were due to cardiovascular disease, cancer and renal failure, respectively. In the multivariable analysis, age per 5-year increase (HR = 1.35; 95% CI: 1.30, 1.41), and extended family and non-family household members (HR = 2.86; 95% CI: 2.05, 3.98) compared to household heads were associated with a significantly increased hazard of NCD mortality. Although the difference was not statistically significant, compared to poor adults, those who were wealthy had a 15% (HR = 0.85; 95% CI: 0.65, 1.11) lower hazard of mortality from NCDs. On the other hand, literate adults (HR = 0.35; 95% CI: 0.13, 0.9) had a significantly decreased hazard of NCD attributed mortality compared to those adults who were unable to read and write. The effect of literacy was modified by age and its effect reduced by 18% for every 5-year increase of age among literate adults.

CONCLUSION

In summary, the study indicates that double mortality burden from both NCDs and communicable diseases was evident in northern rural Ethiopia. Public health intervention measures that prioritise disadvantaged NCD patients such as those who are unable to read and write, the elders, the extended family and non-family household co-residents could significantly reduce NCD mortality among the adult population.

Mutation in sorghum LOW GERMINATION STIMULANT 1 alters strigolactones and causes Striga resistance

Striga is a major biotic constraint to sorghum production in semiarid tropical Africa and Asia. Genetic resistance to this parasitic weed is the most economically feasible control measure. Mutant alleles at the LGS1 (LOW GERMINATION STIMULANT 1) locus drastically reduce Striga germination stimulant activity. We provide evidence that the responsible gene at LGS1 codes for an enzyme annotated as a sulfotransferase and show that functional loss of this gene results in a change of the dominant strigolactone (SL) in root exudates from 5-deoxystrigol, a highly active Striga germination stimulant, to orobanchol, an SL with opposite stereochemistry. Orobanchol, although not previously reported in sorghum, functions in the multiple SL roles required for normal growth and environmental responsiveness but does not stimulate germination of Striga This work describes the identification of a gene regulating Striga resistance and the underlying protective chemistry resulting from mutation.

Cellular Response to the high protein digestibility/high-Lysine (hdhl) sorghum mutation

A high protein digestibility/high-lysine mutant P721Q (hdhl) with a multi-folded protein body morphology has been developed, with a 22kDa α-kafirin single point mutation having also been recently identified. Relatively little is known regarding the resulting cellular response in hdhl endosperm. The aim is to elucidate these biochemical changes. Two-dimentional gel electrophoresis showed an apparent increase of non-kafirin and a decrease in kafirins content in hdhl endosperm. Mass spectrometry data yielded the identity of differentially expressed non-kafirin proteins in hdhl, wild-type lines such as cytoskeleton and chaperones proteins, and also others involved in amino acids and carbohydrates biochemical synthesis pathways. Western blot analysis showed that chaperone proteins were more highly expressed in the hdhl than the wild-type sorghum and confirmed the non-kafirin proteins proteomic results. Two-dimentional gel electrophoresis showed that the γ-kafirin subunits content had decreased, and the 22kDa α-kafirin subunit was increased in hdhl without any apparent molecular mass change. The observed differential expression most likely led to proteins interactions between γ- and α-kafirin subunits in particular, which resulted in a kafirins packing differently to form the protein body's multi-folded morphology, while also improving its digestibility.

Molecular tagging and validation of microsatellite markers linked to the low germination stimulant gene (lgs) for Striga resistance in sorghum [Sorghum bicolor (L.) Moench]

Striga is a devastating parasitic weed in Africa and parts of Asia. Low Striga germination stimulant activity, a well-known resistance mechanism in sorghum, is controlled by a single recessive gene (lgs). Molecular markers linked to the lgs gene can accelerate development of Striga-resistant cultivars. Using a high density linkage map constructed with 367 markers (DArT and SSRs) and an in vitro assay for germination stimulant activity towards Striga asiatica in 354 recombinant inbred lines derived from SRN39 (low stimulant) × Shanqui Red (high stimulant), we precisely tagged and mapped the lgs gene on SBI-05 between two tightly linked microsatellite markers SB3344 and SB3352 at a distance of 0.5 and 1.5 cM, respectively. The fine-mapped lgs region was delimited to a 5.8 cM interval with the closest three markers SB3344, SB3346 and SB3343 positioned at 0.5, 0.7 and 0.9 cM, respectively. We validated tightly linked markers in a set of 23 diverse sorghum accessions, most of which were known to be Striga resistant, by genotyping and phenotyping for germination stimulant activity towards both S. asiatica and S. hermonthica. The markers co-segregated with Striga germination stimulant activity in 21 of the 23 tested lines. The lgs locus similarly affected germination stimulant activity for both Striga species. The identified markers would be useful in marker-assisted selection for introgressing this trait into susceptible sorghum cultivars. Examination of the sorghum genome sequence and comparative analysis with the rice genome suggests some candidate genes in the fine-mapped region (400 kb) that may affect strigolactone biosynthesis or exudation. This work should form a foundation for map-based cloning of the lgs gene and aid in elucidation of an exact mechanism for resistance based on low Striga germination stimulant activity.

African Green Revolution needn't be a mirage

Africa missed out on the scientific breakthroughs that revolutionized agriculture in Asia. However, with locally developed and locally relevant technologies, a built-up human and institutional capacity, and supportive national policy and leadership, an African Green Revolution can be a reality.

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.

Distribution of brucellosis among small ruminants in the pastoral region of Afar, eastern Ethiopia

A cross-sectional study was conducted in the pastoral region of Afar, in eastern and central Ethiopia, to determine the distribution of brucellosis in small ruminants. Between December 2005 and June 2006, 1,568 serum samples were taken: 563 samples from sheep and 1,005 from goats. One hundred and forty-seven of these (9.4%) tested positive using the Rose Bengal plate test (RBPT), and 76 (4.8%) also tested positive by the complement fixation test (CFT). Brucellosis was detected in all five administrative zones of the region. The difference in prevalence (P) among the zones was not statistically significant (P > 0.05). The seroprevalence of Brucella infection was found to be 5.8% (n = 58) in goats and 3.2% (n = 18) in sheep. A prevalence rate of 5.3% was observed in adult animals and 1.6% in younger sheep and goats. Caprine species (chi2 = 5.56) and adult goats and sheep (chi2 = 4.84) were found to be at higher risk of Brucella infection (P < 0.05). No statistically significant difference was found between males and females (chi2 = 2.57, P > 0.05). The study showed that small-ruminant brucellosis is a widely distributed disease in Afar. The authors recommend the implementation of well-organised disease control and prevention methods to mitigate the economic losses and public health hazard caused by the disease.

Marker-assisted selection for early-season cold tolerance in sorghum: QTL validation across populations and environments

Sorghum [Sorghum bicolor (L.) Moench] landraces from China generally exhibit excellent emergence and seedling vigor under cool conditions, and are being used as sources of genes for improvement of seedling cold tolerance in other cultivars. Marker-assisted selection (MAS) could expedite the introgression of genes from landraces into elite lines, however, only a few studies have empirically demonstrated efficacy of MAS for quantitatively inherited agronomic traits. In a preceding study we identified quantitative trait loci (QTL) for early-season performance in a recombinant inbred (RI) population, one parent of which was a cold-tolerant Chinese line, 'Shan Qui Red' (SQR). In this study, three SSR markers (Xtxp43, Xtxp51, and Xtxp211), each representing a QTL, were tested in two new populations: (Tx2794 x SQR F(3)) and (Wheatland x SQR BC(1)F(3)). Individual families were genotyped, and early-season field performance was measured for two years. Statistical analyses showed that the SQR allele of Xtxp43 had favorable effects on seedling vigor in both populations, and on emergence in the Tx2794 population. A large positive effect of the SQR allele of Xtxp51 was observed in the Tx2794 population for vigor and emergence. Slight genotype by environment interaction was observed for Xtxp51 in the Wheatland population. Marker Xtxp211 had small but significant effects on seedling vigor and emergence in both populations. Various interactions between loci were also significant. This study validated QTL markers in various genetic backgrounds, and demonstrated the utility of MAS for a quantitative trait, early-season cold tolerance, evaluated in the field.

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.

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.

Characterization of carotenoid pigments in mature and developing kernels of selected yellow-endosperm sorghum varieties

Sorghum is a critical source of food in the semiarid regions of sub-Saharan Africa and India and a potential source of dietary phytochemicals including carotenoids. The objective of this study was to determine the carotenoid profiles of sorghum cultivars, selected on the basis of their yellow-endosperm kernels, at various developmental stages. Following extraction from sorghum flours, carotenoids were separated by high-performance liquid chromatography (HPLC) with diode array detection. Total carotenoid content in fully matured yellow-endosperm sorghum kernels (0.112-0.315 mg/kg) was significantly lower (p < 0.05) than that in yellow maize (1.152 mg/kg) at physiological maturity. Variation in total carotenoids and within individual carotenoid species was observed in fully mature sorghum cultivars. For developing kernels, large increases in carotenoid content occurred between 10 and 30 days after half bloom (DAHB), resulting in a peak accumulation between 6.06 and 28.53 microg of total carotenoids per thousand kernels (TK). A significant (p < 0.05) decline was noted from 30 to 50 DAHB, resulting in a final carotenoid content of 2.62-15.02 microg/TK total carotenoids. (all-E)-Zeaxanthin was the most abundant carotenoid, ranging from 2.22 to 13.29 microg/TK at 30 DAHB. (all-E)-Beta-carotene was present in modest amounts (0.15-3.83 microg/TK). These data suggest the presence of genetic variation among sorghum cultivars for carotenoid accumulation in developing and mature kernels.

Nutritional evaluation of high-digestible sorghum for pigs and broiler chicks

Two experiments were conducted to evaluate the nutritional quality of 2 varieties of Purdue high-digestible sorghum (PHD1 and PHD2) and a normal sorghum, compared with corn, in diets of pigs and broiler chicks. In Exp. 1, 12 pigs (average BW, 55 kg) fitted with ileal T-cannula were fed 4 diets containing 946 g of corn or sorghum (PHD1, PHD2, and normal) per kg in a 2-period crossover design (i.e., each pig received 2 diets over a 2-wk period with 6 pigs per dietary treatment) to determine apparent ileal or total tract digestibility of nutrients and energy. There was no difference in the ileal or total tract digestibility of DM, energy, P, Ca, or N among dietary treatments. In Exp. 2, a total of 192 broiler chicks were grouped by weight into 8 blocks of 4 cages each with 6 chicks per cage, and cages were assigned randomly to 1 of the 4 dietary treatments within each block. Chicks were fed corn-soybean meal (SBM) or sorghum-SBM diets for 21 d to determine apparent total tract retention and then switched to diets containing 935 g of the corresponding corn or 1 of the 3 sorghum varieties per kg for 7 d to determine apparent ileal digestibility and total tract retention. Apparent ileal digestibilities of DM and P, as well as energy, were not different in chicks fed diets containing 935 g of corn or 1 of the 3 sorghum varieties per kg. However, apparent total tract retention of DM, energy, and N in chicks fed corn was greater (P < 0.05) than those fed 1 of the 3 sorghum varieties. Although the apparent ME content of corn was greater than PHD1 and normal sorghum (P < 0.01), it was not different from PHD2 sorghum. There was no difference in apparent total tract retention of DM between chicks fed the corn-SBM and PHD-SBM diets, but it was greater (P < 0.05) in chicks fed the corn-SBM diet than those fed the normal sorghum-SBM diet. Apparent total tract retention of N in chicks fed the PHD1-SBM diet was lower (P < 0.05) than in those fed the corn-SBM diet but greater (P < 0.05) than in chicks fed the normal sorghum-SBM meal diet. No difference in the apparent ME content between the corn-SBM and PHD2-SBM diets was observed, but it was greater (P < 0.05) for the corn-SBM diet than the PHD1- or normal sorghum-SBM diet. Weight gain, feed intake, and feed efficiency were not different in chicks fed the corn-SBM or sorghum-SBM diets. Sorghum could serve as a substitute for corn in cereal grain-SBM diets for pigs and broiler chicks.

The effects of tannins on nutrient utilisation in the White Pekin duck

1. Two experiments were conducted to determine the effects of tannins on nutrient utilisation in the White Pekin duck. 2. Experiment 1 was a rapid nutrient balance assay to determine the nitrogen (N) retention and metabolisable energy (ME) of maize, low-tannin sorghum (P-954063) (Sorghum bicolor (L). Moench) and high-tannin sorghum (IS-4225) cultivars for ducks. The assay lasted 120 h, with an initial 24 h food-deprivation period, a 48 h excreta collection period for endogenous losses and a 48 h excreta collection period for ingredient losses. The true metabolisable energy (TMEn) content was lower (P<0.05) in the high-tannin sorghum cultivar (13.85 MJ/kg) than the maize (14.94 MJ/kg) and the low-tannin sorghum cultivar (14.39 MJ/kg). True N retention was lower (P<0.05) for the high-tannin sorghum (0.24 g) than for maize (1.33 g) and low-tannin sorghum (1.1 g). 3. In experiment 2, the brush-border membrane vesicles technique was used to determine whether tannic acid caused inhibition of L-threonine transport across duck intestinal brush-border membrane. The brush-border membrane vesicles were mixed with tannic acid solutions (pH 7.4) to give gradient tannic acid concentrations of 0, 0.05, 0.10, 0.25, 0.50, 1.00 and 2.50%. As a fraction of the control (no tannic acid), the maximal inhibition of L-threonine transport (Imax) under the sodium-gradient condition was 77.10% (P<0.05). Under the sodium-free condition, the maximal inhibition of L-threonine transport (Imax) was 45.15% (P<0.05). 4. These results demonstrated that nutrient utilisation in the White Pekin duck was lower from the high-tannin sorghum cultivar than from the low-tannin sorghum cultivar. The results also suggested that the antinutritive effects of tannins in foodstuffs are due partly to their inhibitory action on intestinal brush-border bound amino acid transporter proteins.

Screening for grain polyphenol variants from high-tannin sorghum somaclones

Several hundred somaclones established from plants regenerated from embryogenic callus cultures of six high tannin sorghum lines were screened for variants with altered levels of polyphenols in the grain. Grain from over 6000 plants including the R 1 (primary), R2, and R3 generations were analyzed for total phenols, flavan-4-ols, and proanthocyanidins (condensed tannins). Although many variants which had lost the ability to synthesize chlorophyll were found, none of the somaclones tested had lost or greatly reduced the ability to synthesize any of the polyphenols assayed. However, we did observe statistically significant differences in polyphenol concentration between tissue culture-derived R1 plants and the parental controls. In the R2 generation the proportion of somaclones which differed significantly from the parents varied from 47% to 68% depending upon genotype. The average somaclonal variation rate and somaclonal variant frequency estimated in the tested population for the three polyphenol characteristics ranged from 37.3% to 40.7% and 5.3% to 7.8%, respectively. Variants with decreased levels of polyphenols were usually epigenetic and reverted back to normal levels in subsequent generations, but those with increased levels usually persisted after two meiotic cycles, indicating they are heritable. Variants with polyphenol levels increased up to 80% or decreased by 30% were selected for in the R3 generation.

Development and maturation of surghum seeds on detached panicles grown in vitro

A procedure for culturing detached panicles of sorghum, Sorghum bicolor (L.) Moench, was developed to achieve flowering, fertilization, and subsequent seed development and maturation in vitro. Sixteen sorghum genotypes (five high and eleven low in tannin) were tested for their ability to develop normally in culture. Panicles collected one to two days before the initiation of anthesis were cultured in flasks containing liquid medium. Contamination and medium darkening were the major obstacles encountered. Up to 55% of the panicles cultured reached physiological maturity in vitro. The frequency of seed set ranged from 30 to 97% depending upon genotype and medium. Seed and glume color were normal. Seed produced in vitro resembled those grown in vivo and germinated well, but were smaller than normal (100 kernel weight reached 50 to 70% of the control). Grain polyphenols were synthesized in the cultured panicles. Seed of high tannin genotypes produced in vitro were lower in total phenols and tannins and higher in flavan-4-ols and the 3-deoxyanthocyanidin pigments than control seed. This technique can be used for harvesting late-maturing stocks and for various sorghum studies.

Somaclonal variation in high tannin sorghums

Genetic variants were found among over 6,000 primary plants (R1) regenerated from embryogenic tissue cultures of eight high tannin sorghums [Sorghum bicolor (L.) Moench]. Field assessment of somaclonal variation has progressed to the R2 population, with over 48,000 R2 seedlings (27,000 plants) in 1,126 rows from 1,055 R1 plants. A total of 43 variant phenotypes was recovered, including several types of chlorophyll deficiencies, dwarfism, short culm, sterility, narrow leaf, and several previously unreported variants, such as ragged leaf, multibranched heads, and Hydra, a developmental variant which produces large numbers of panicles. Variation production greatly depends on parent genotype and appears to increase with increasing time in cultures. The toal average somaclonal variation rate (based per 100 R1 plants) and somaclonal variant frequency (based per 100 R2 plants) estimated in the tested population were 11.3 and 1.6, respectively. Chimerism was found in regenerants. The estimated size of the mutated sector carried by mutant regenerants ranged from the whole plant to less than 3% of a single head. The average proportion of mutated R1 heads carrying large (80%-100%), medium (40%-80%), and small (<40%) mutated sectors was 38.7%, 26.0% and 35.3%, respectively. Some sector mutations do not appear until the R3 generation. In order to avoid losing variants, the population for selecting somaclonal variation should be as large as possible. Some of these variants found may be useful for further study or for use in breeding programs.

In vitro digestibility and amino acid composition of pearl millet (Pennisetum typhoides) and other cereals

The purpose of this study was to compare in vitro digestibility, protein distribution patterns, and amino acid composition of pearl millet with other major cereals. Digestibility values for the pearl millet varieties were higher than that of sorghum and comparable to that of maize. In contrast to sorghum, digestibility of pearl millet and maize did not decrease significantly upon cooking. Protein distribution patterns of uncooked pearl millet and shifts in the different fractions as a result of cooking also resembled that of maize and not sorghum. The amino acid profile of pearl millet is more favorable than that of normal sorghum and normal maize and is comparable to the small grains, wheat, barley, and rice. On the basis of these findings, it appears that pearl millet is a nutritious and well-digested source of calories and proteins for humans.