Genetic diversity among early provitamin A quality protein maize inbred lines and the performance of derived hybrids under contrasting nitrogen environments.

BACKGROUND: Information on population structure and genetic diversity of germplasm in a breeding programme is useful because it enhances judicious utilisation of genetic resources to achieve breeding objectives. Seventy early maturing provitamin A (PVA) quality protein maize (QPM) inbreds developed by the IITA- maize improvement programme were genotyped using 8171 DArTseq markers. Furthermore, 96 hybrids derived from 24 selected inbreds plus four checks were evaluated under low-N and optimal environments in Nigeria during 2016 and 2017. Genotypic and phenotypic data of inbreds and hybrids respectively, were analysed to (i) assess the level of genetic dissimilarities and population structure of the inbreds, and (ii) investigate the grain yield performance of derived hybrids under low-N, optimal and across environments. RESULTS: Genetic diversity among the seventy inbreds was high varying from 0.042 to 0.500 with an average of 0.357. Sixty-six inbred lines with probabilities ≥0.70 were assigned to a single group. The population structure analysis, the UPGMA phylogeny, and the principal Coordinate Analysis (PCoA) of the DArTseq markers revealed a clear separation of five groups and each followed pedigree records. Clustered inbreds displayed common characteristics including high PVA levels, and drought and low-N tolerance. The top performing hybrid, TZEIORQ 40 × TZEIORQ 26 out-yielded the best hybrid control, TZEIOR 127 × TZEIOR 57 by 8, 3, and 9% under low-N, optimal, and across environments, respectively. High repeatability estimates were detected for grain yield under each and across environments. Similarly, high breeding efficiency of 71, 70 and 72% were computed under low-N, optimal, and across environments, respectively. CONCLUSIONS: The UPGMA clustering, the structure analysis, and the PCoA consistently revealed five groups which largely followed pedigree information indicating the existence of genetically distinct groups in the inbred lines. High repeatability and breeding efficiency values estimated for grain yield of hybrids under low-N, optimal and across environments demonstrated that high productive hybrids could be developed using inbreds from the opposing clusters identified by the DArTseq markers. The 15 top performing hybrids identified, particularly TZEIORQ 40 × TZEIORQ 26 and TZEIORQ 29 × TZEIORQ 43 should be further evaluated for release and commercialization in SSA.

Assessing inbred-hybrid relationships for developing drought-tolerant provitamin A-quality protein maize hybrids.

Drought-tolerant early-maturing maize (Zea mays L.) inbred lines with high levels of provitamin A (PVA) and quality protein (QPM) are urgently needed for development of superior hybrids to mitigate malnutrition and to intensify maize production and productivity in sub-Saharan Africa (SSA). This study was designed to identify early-maturing inbred lines with combined tolerance to drought, elevated tryptophan, and PVA contents; to examine inbred-hybrid relationships for tryptophan and PVA accumulation; and to select hybrids with outstanding grain yield (GY) performance. A total of 64 inbred lines and six checks, plus 96 hybrids and four checks, were evaluated under drought and well-watered environments in Nigeria for 2 yr. Eighteen parental lines and 54 derived hybrids were assayed for tryptophan and PVA contents. Ten drought-tolerant inbred lines with high tryptophan and elevated PVA levels were identified in the top 10 hybrid combinations across managed drought and well-watered conditions. The inbred-hybrid relationship was significant for GY under each and across the two contrasting environments. Significant average heterosis was found for tryptophan and PVA under well-watered conditions. This indicated that the selected inbred lines could be used for developing high-yielding PVA-QPM hybrids tolerant to drought stress in SSA. The 10 top-performing PVA-QPM hybrids identified are being extensively evaluated in different locations and subsequently in on-farm trials for commercialization throughout SSA.

Genetic characterization of cassava (Manihot esculenta Crantz) genotypes using agro-morphological and single nucleotide polymorphism markers.

Dearth of information on extent of genetic variability in cassava limits the genetic improvement of cassava genotypes in Sierra Leone. The aim of this study was to assess the genetic diversity and relationships within 102 cassava genotypes using agro-morphological and single nucleotide polymorphism markers. Morphological classification based on qualitative traits categorized the germplasm into five different groups, whereas the quantitative trait set had four groups. The SNP markers classified the germplasm into three main cluster groups. A total of seven principal components (PCs) in the qualitative and four PCs in the quantitative trait sets accounted for 79.03% and 72.30% of the total genetic variation, respectively. Significant and positive correlations were observed between average yield per plant and harvest index (r = 0.76***), number of storage roots per plant and harvest index (r = 0.33*), height at first branching and harvest index (0.26*), number of storage roots per plant and average yield per plant (r = 0.58*), height at first branching and average yield per plant (r = 0.24*), length of leaf lobe and petiole length (r = 0.38*), number of leaf lobe and petiole length (r = 0.31*), width of leaf lobe and length of leaf lobe (r = 0.36*), number of leaf lobe and length of leaf lobe (r = 0.43*), starch content and dry matter content (r = 0.99***), number of leaf lobe and root dry matter (r = 0.30*), number of leaf lobe and starch content (r = 0.28*), and height at first branching and plant height (r = 0.45**). Findings are useful for conservation, management, short term recommendation for release and genetic improvement of the crop.

Farmers' production constraints, preferred varietal traits and perceptions on sorghum grain mold in Senegal.

Improving sorghum adoption rates by developing adapted varieties that meet end-user preferences is a major challenge in West Africa. In this study, a participatory rural appraisal was undertaken to identify the main sorghum production constraints, farmers' preferred variety traits and their perceptions on sorghum grain mold. The study was conducted in four representative rural communities located in the main sorghum producing area of Senegal. A total of 260 farmers were interviewed and data were collected through focus group discussions and individual questionnaires. Our results indicated that Striga, insects, poor soil fertility and drought are the major sorghum producing constraints in Senegal. Grain mold was identified as the second most important sorghum disease after the damping-off. Discoloration on grain surface was the most important criteria farmers used to recognize the disease. The most important sorghum traits farmers desired in improved varieties are medium to short plant maturity cycle, medium plant height, large open or semi-compact panicle, big and white grain, and adaptation to local growing conditions. The results showed that the sorghum cropping system is dominated by male farmers who mainly grow local landraces. These results will provide updated recommendations for the breeding products profile to meet end-user preferences in Senegal.

Genetic diversity and epidemic histories of rice yellow mottle virus in Ghana.

Rice yellow mottle virus (RYMV) has persisted as a major biotic constraint to rice production in Africa. However, no data on RYMV epidemics were available in Ghana, although it is an intensive rice-producing country. Surveys were performed from 2010 to 2020 in eleven rice-growing regions of Ghana. Symptom observations and serological detections confirmed that RYMV is circulating in most of these regions. Coat protein gene and complete genome sequencings revealed that RYMV in Ghana almost exclusively belongs to the strain S2, one of the strains covering the largest area in West Africa. We also detected the presence of the S1ca strain which is being reported for the first time outside its area of origin. These results suggested a complex epidemiological history of RYMV in Ghana and a recent expansion of S1ca to West Africa. Phylogeographic analyses reconstructed at least five independent RYMV introductions in Ghana for the last 40 years, probably due to rice cultivation intensification in West Africa leading to a better circulation of RYMV. In addition to identifying some routes of RYMV dispersion in Ghana, this study contributes to the epidemiological surveillance of RYMV and helps to design disease management strategies, especially through breeding for rice disease resistance.

Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm.

Maize (Zea mays L.) production is constrained by drought and heat stresses. The combination of these two stresses is likely to be more detrimental. To breed for maize cultivars tolerant of these stresses, 162 tropical maize inbred lines were evaluated under combined heat and drought (CHD) and terminal drought (TD) conditions. The mixed linear model was employed for the genome-wide association study using 7834 SNP markers and several phenotypic data including, days to 50% anthesis (AD) and silking (SD), husk cover (HUSKC), and grain yield (GY). In total, 66, 27, and 24 SNPs were associated with the traits evaluated under CHD, TD, and their combined effects, respectively. Of these, four single nucleotide polymorphism (SNP) markers (SNP_161703060 on Chr01, SNP_196800695 on Chr02, SNP_195454836 on Chr05, and SNP_51772182 on Chr07) had pleiotropic effects on both AD and SD under CHD conditions. Four SNPs (SNP_138825271 (Chr03), SNP_244895453 (Chr04), SNP_168561609 (Chr05), and SNP_62970998 (Chr06)) were associated with AD, SD, and HUSKC under TD. Twelve candidate genes containing phytohormone cis-acting regulating elements were implicated in the regulation of plant responses to multiple stress conditions including heat and drought. The SNPs and candidate genes identified in the study will provide invaluable information for breeding climate smart maize varieties under tropical conditions following validation of the SNP markers.

Combining Ability and Heterotic Patterns of Tropical Early-Maturing Maize Inbred Lines under Individual and Combined Heat and Drought Environments.

Information on combining ability and heterotic patterns of multiple stress-tolerant inbred lines are fundamental prerequisites for devising appropriate breeding strategies for the development of climate-resilient maize hybrids. In the present study, we evaluated 150 single cross hybrids derived from the North Carolina Design II (NCD II) along with six commercial checks under terminal drought stress (TDS), heat stress (HS), and combined drought and heat stress (CHDS)conditions. The objectives of the study were to: (i) determine the combining ability of the inbred lines and identify the best testers across the stresses; (ii) classify the inbred lines into heterotic groups (HGs) based on the general combining ability of multiple traits (HGCAMT) and sequencing-based diversity array technology (DArTseq) and (iii) assess the performance and stability of the lines in hybrid combinations. The inbred lines showed significantly (p < 0.01 and p < 0.05) positive and negative general combining ability (GCA) and specific combining ability (SCA) effects for grain yield (GY) and most other measured traits. The inbred line TZEI 135 displayed relatively larger positive GCA effects for GY when mated either as male or female and was identified as the best tester. TZEI 135 × TZEI 182 was identified as the best single-cross tester across environments. Results of the assessment of the relative importance of GCA and SCA effects revealed the predominance of additive gene action over the non-additive. Six HGs of inbreds were identified using the HGCAMT and three, based on the DArTseq marker genetic distance method, were the most efficient. The best hybrids in this study significantly out-yielded the best checks by 21, 46, and 70% under CHDS, HS, and TDS, respectively. These hybrids should be extensively tested in on-farm trials for possible commercialization in sub-Saharan Africa.

Identification of Genomic Regions Associated with Agronomic and Disease Resistance Traits in a Large Set of Multiple DH Populations.

Breeding maize lines with the improved level of desired agronomic traits under optimum and drought conditions as well as increased levels of resistance to several diseases such as maize lethal necrosis (MLN) is one of the most sustainable approaches for the sub-Saharan African region. In this study, 879 doubled haploid (DH) lines derived from 26 biparental populations were evaluated under artificial inoculation of MLN, as well as under well-watered (WW) and water-stressed (WS) conditions for grain yield and other agronomic traits. All DH lines were used for analyses of genotypic variability, association studies, and genomic predictions for the grain yield and other yield-related traits. Genome-wide association study (GWAS) using a mixed linear FarmCPU model identified SNPs associated with the studied traits i.e., about seven and eight SNPs for the grain yield; 16 and 12 for anthesis date; seven and eight for anthesis silking interval; 14 and 5 for both ear and plant height; and 15 and 5 for moisture under both WW and WS environments, respectively. Similarly, about 13 and 11 SNPs associated with gray leaf spot and turcicum leaf blight were identified. Eleven SNPs associated with senescence under WS management that had depicted drought-stress-tolerant QTLs were identified. Under MLN artificial inoculation, a total of 12 and 10 SNPs associated with MLN disease severity and AUDPC traits, respectively, were identified. Genomic prediction under WW, WS, and MLN disease artificial inoculation revealed moderate-to-high prediction accuracy. The findings of this study provide useful information on understanding the genetic basis for the MLN resistance, grain yield, and other agronomic traits under MLN artificial inoculation, WW, and WS conditions. Therefore, the obtained information can be used for further validation and developing functional molecular markers for marker-assisted selection and for implementing genomic prediction to develop superior elite lines.

Genetic diversity and inter-trait relationship of tropical extra-early maturing quality protein maize inbred lines under low soil nitrogen stress.

Information on the genetic diversity, population structure, and trait associations of germplasm resources is crucial for predicting hybrid performance. The objective of this study was to dissect the genetic diversity and population structure of extra-early yellow and orange quality protein maize (QPM) inbred lines and identify secondary traits for indirect selection for enhanced grain yield under low-soil nitrogen (LN). One hundred and ten inbred lines were assessed under LN (30 kg ha -1) and assayed for tryptophan content. The lines were genotyped using 2500 single nucleotide polymorphism (SNP) markers. Majority (85.4%) of the inbred lines exhibited wide pairwise genetic distances between 0.4801 and 0.600. Genetic distances were wider between yellow and orange endosperm lines and predicted high heterosis in crosses between parents of different endosperm colors. The unweighted pair group method with arithmetic mean (UPGMA) and the admixture model-based population structure method both grouped the lines into five clusters. The clustering was based on endosperm color, pedigree, and selection history but not on LN tolerance or tryptophan content. Genotype by trait biplot analysis revealed association of grain yield with plant height and ear height. TZEEQI 394 and TZEEIORQ 73A had high expressivity for these traits. Indirect selection for high grain yield among the inbred lines could be achieved using plant and ear heights as selection criteria. The wide genetic variability observed in this study suggested that the inbred lines could be important sources of beneficial alleles for LN breeding programs in SSA.

Introgression of Maize Lethal Necrosis Resistance Quantitative Trait Loci Into Susceptible Maize Populations and Validation of the Resistance Under Field Conditions in Naivasha, Kenya.

Maize lethal necrosis (MLN), resulting from co-infection by maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV) can cause up to 100% yield losses in maize in Africa under serious disease conditions. Maize improvement through conventional backcross (BC) takes many generations but can significantly be shortened when molecular tools are utilized in the breeding process. We used a donor parent (KS23-6) to transfer quantitative trait loci (QTL) for resistance to MLN into nine adapted but MLN susceptible lines. Nurseries were established in Kiboko, Kenya during 2015-2017 seasons and BC3F2 progeny were developed using marker assisted backcrossing (MABC) approach. Six single nucleotide polymorphism (SNP) markers linked to QTL for resistance to MLN were used to genotype 2,400 BC3F2 lines using Kompetitive Allele Specific PCR (KASP) platform. We detected that two of the six QTL had major effects for resistance to MLN under artificial inoculation field conditions in 56 candidate BC3F2 lines. To confirm whether these two QTL are reproducible under different field conditions, the 56 BC3F2 lines including their parents were evaluated in replicated trials for two seasons under artificial MLN inoculations in Naivasha, Kenya in 2018. Strong association of genotype with phenotype was detected. Consequently, 19 superior BC3F2 lines with favorable alleles and showing improved levels of resistance to MLN under artificial field inoculation were identified. These elite lines represent superior genetic resources for improvement of maize hybrids for resistance to MLN. However, 20 BC3F2 lines were fixed for both KASP markers but were susceptible to MLN under field conditions, which could suggest weak linkage between the KASP markers and target genes. The validated two major QTL can be utilized to speed up the breeding process but additional loci need to be identified between the KASP markers and the resistance genes to strengthen the linkage.

Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers.

Striga hermonthica is a serious biotic stress limiting maize production in sub-Saharan Africa. The limited information on the patterns of genetic diversity among maize inbred lines derived from source germplasm with mixed genetic backgrounds limits the development of inbred lines, hybrids, and synthetics with durable resistance to S. hermonthica. This study was conducted to assess the level of genetic diversity in a panel of 150 diverse maize inbred lines using agronomic and molecular data and also to infer the population structure among the inbred lines. Ten Striga-resistance-related traits were used for the phenotypic characterization, and 16,735 high-quality single-nucleotide polymorphisms (SNPs), identified by genotyping-by-sequencing (GBS), were used for molecular diversity. The phenotypic and molecular hierarchical cluster analyses grouped the inbred lines into five clusters, respectively. However, the grouping patterns between the phenotypic and molecular hierarchical cluster analyses were inconsistent due to non-overlapping information between the phenotypic and molecular data. The correlation between the phenotypic and molecular diversity matrices was very low (0.001), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and molecular diversity analyses. The joint phenotypic and genotypic diversity matrices grouped the inbred lines into three groups based on their reaction patterns to S. hermonthica, and this was able to exploit a broad estimate of the actual diversity among the inbred lines. The joint analysis shows an invaluable insight for measuring genetic diversity in the evaluated materials. The result indicates that wide genetic variability exists among the inbred lines and that the joint diversity analysis can be utilized to reliably assign the inbred lines into heterotic groups and also to enhance the level of resistance to Striga in new maize varieties.

Phenotypic characterization and validation of provitamin A functional genes in early maturing provitamin A-quality protein maize (Zea mays) inbred lines.

The number of drought and low-N tolerant hybrids with elevated levels of provitamin A (PVA) in sub-Saharan Africa could increase when PVA genes are optimized and validated for developed drought and low-N tolerant inbred lines. This study aimed to (a) determine the levels of drought and low-N tolerance, and PVA concentrations in early maturing PVA-quality protein maize (QPM) inbred lines, and (b) identify lines harbouring the crtRB1 and LcyE genes as sources of favourable alleles of PVA. Seventy early maturing PVA-QPM inbreds were evaluated under drought, low-N and optimal environments in Nigeria for two years. The inbreds were assayed for PVA levels and the presence of PVA genes using allele-specific PCR markers. Moderate range of PVA contents was observed for the inbreds. Nonetheless, TZEIORQ 55 combined high PVA concentration with drought and low-N tolerance. The crtRB1-3'TE primer and the KASP SNP (snpZM0015) consistently identified nine inbreds including TZEIORQ 55 harbouring the favourable alleles of the crtRB1 gene. These inbreds could serve as donor parents of the favourable crtRB1-3'TE allele for PVA breeding in maize.

Genetic Analysis of QTL for Resistance to Maize Lethal Necrosis in Multiple Mapping Populations.

Maize lethal necrosis (MLN) occurs when maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV) co-infect maize plant. Yield loss of up to 100% can be experienced under severe infections. Identification and validation of genomic regions and their flanking markers can facilitate marker assisted breeding for resistance to MLN. To understand the status of previously identified quantitative trait loci (QTL)in diverse genetic background, F3 progenies derived from seven bi-parental populations were genotyped using 500 selected kompetitive allele specific PCR (KASP) SNPs. The F3 progenies were evaluated under artificial MLN inoculation for three seasons. Phenotypic analyses revealed significant variability (P ≤ 0.01) among genotypes for responses to MLN infections, with high heritability estimates (0.62 to 0.82) for MLN disease severity and AUDPC values. Linkage mapping and joint linkage association mapping revealed at least seven major QTL (qMLN3_130 and qMLN3_142, qMLN5_190 and qMLN5_202, qMLN6_85 and qMLN6_157qMLN8_10 and qMLN9_142) spread across the 7-biparetal populations, for resistance to MLN infections and were consistent with those reported previously. The seven QTL appeared to be stable across genetic backgrounds and across environments. Therefore, these QTL could be useful for marker assisted breeding for resistance to MLN.

Seasonal variation in Hibiscus sabdariffa (Roselle) calyx phytochemical profile, soluble solids and α-glucosidase inhibition.

Seasonal variations in crops can alter the profile and amount of constituent compounds and consequentially any biological activity. Differences in phytochemical profile, total phenolic content and inhibitory activity on α-glucosidase (maltase) of Hibiscus sabdariffa calyces grown in South Western Nigeria were determined over wet and dry seasons. The phenolic profile, organic acids and sugars were analysed using HPLC, while inhibition of rat intestinal maltase was measured enzymically. There was a significant increase (1.4-fold; p ≤ 0.05) in total anthocyanin content in the dry compared to wet planting seasons, and maltase inhibition from the dry season was slightly more potent (1.15-fold, p ≤ 0.05). Fructose (1.8-fold), glucose (1.8-fold) and malic acid (3.7-fold) were significantly higher (p ≤ 0.05) but citric acid was lower (62-fold, p ≤ 0.008) in the dry season. Environmental conditions provoke metabolic responses in Hibiscus sabdariffa affecting constituent phytochemicals and nutritional value.