Comparison between random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers with high resolution melt analyses in genetic variation analysis among selected sorghum genotypes

Understanding the genetic diversity of germplasm is essential in plant breeding programmes and germplasm management. Molecular markers are efficient and effective tools widely used for assessing genetic diversity among crop genotypes. Recently, high resolution melt analysis (HRM) has been reported for detecting genetic variability. However, there is limited information on the use of HRM in conjunction with other molecular marker techniques for assessing genetic variation in sorghum [Sorghum bicolor (L.) Moench]. This study was conducted to compare random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers with HRM analyses to determine genetic variation among selected sorghum genotypes. Eight diverse sorghum accessions obtained from the plant genetic resources, Department of Agriculture, Forestry and Fisheries/South Africa were subjected to both analyses. DNA was extracted from fresh leaves of the eight accessions and amplified using three RAPD and three SSR primers. The HRM analysis was performed and temperature normalised melting curves and difference plots were created and results compared. Both the molecular markers and HRM revealed variations among the accessions. The HRM melting profiles fairly well correlated with results from the RAPD and SSR analysis. The clustering of sorghum accessions using SSR marker highly corresponded with the HRM analysis. Therefore, the HRM can be a useful tool in genetic diversity and classification of sorghum genotypes without post-PCR analysis or processing.Key words: Genetic diversity, high resolution melt analysis, RAPD, simple sequence repeat, sorghum

Development of a single nucleotide polymorphism (SNP) marker for detection of the low phytic acid (lpa1-1) gene used during maize breeding

Breeding for low phytic acid (LPA) in maize is hampered by a tedious and destructive colorimetric assay in mature dry grain. There are no molecular markers available for the single recessive gene of lpa1-1, restricting breeding programmes. The aim of this study is to develop a molecular marker to identify the lpa1-1 gene at the early vegetative plant stage. The parental lines are temperate LPA line (CM 32) and tropical line (P 16). The lpa1-1 allele is due to a single amino acid change from alanine to valine. The nature of the single nucleotide polymorphism (SNP) marker was validated by DNA sequencing of the parental PCR products. Using high resolution melt (HRM) profiles and normalised difference plots, we successfully differentiated the homozygous dominant (wild type), homozygous recessive (LPA) and heterozygous genotypes. The reduced phytate content of the LPA parental line was confirmed. The profiles from low cost crude and high quality DNA extraction were comparable when distinguishing between the parental lines. The cost of HRM analysis was 8% of the cost of PCR amplification and DNA sequencing. The development of the marker will make maize breeding for LPA efficient and fast, and it will enable the earlier release of lpa1-1 varieties.Keywords: High resolution melt (HRM) analysis, low phytic acid, maize, single nucleotide polymorphism (SNP) markerAfrican Journal of Biotechnology Vol. 12(9), pp. 892-90

Evaluation of Bambara groundnut varieties for off-season production in Zimbabwe

Early planting of bambara groundnuts (Vigna subterranea L. Verdc) in the southern Africa enables farmers to fetch premium prices before the markets are flooded with produce from the main summer growing period.However, adaptation of the crop outside the main growing season has not been studied in Zimbabwe. Therefore, this study evaluated 20 varieties at four planting dates covering contrasting temperatures and daylength, at Harare Research Station, during 2000/2001. Planting date was the main plot factor replicated three times and cultivar the subplot. Standard agronomic practices were followed and adequate moisture supplied through supplementary irrigation. Both the planting dates and variety main effects were significant (

Gene action of blast disease reaction and grain yield traits in finger millet

Gene action of blast reaction, yield and yield associated traits in finger millet were studied using a 4x4 North Carolina Design II mating scheme. The four female and four male parents and their 16 crosses were evaluated at Alupe and Kakamega in western Kenya in a randomized complete block design under both artificially induced and natural disease pressure. General combining ability (GCA) and specific combining ability (SCA) estimates of the traits were calculated to determine the genotypes breeding value. The GCA variance predominated over SCA variance for all traits except finger width hence these traits can be improved through selection. With high, desirable GCA effects, male parent KNE 392 and female parents KNE 744 and IE 11 are suitable for blast resistance breeding while male parent Okhale 1 is suitable for grain yield improvement. The frequency distribution for the segregating F2 generation for the three blast types differed within and between crosses which could be due to differences in gene numbers or gene combinations being expressed in the different parents used. Convergent crossing or gene pyramiding for durable resistance could be possible

RESPONSE OF LOCALLY ADAPTED PEARL MILLET POPULATIONS TO S1 PROGENY RECURRENT SELECTION FOR GRAIN YIELD AND RESISTANCE TO RUST

In the semi-arid zones of Uganda, pearl millet ( Pennisetum glaucum (L.) R. Br.) is mainly grown for food and income; but rust (Puccinia substriata var indica (L.) R. Br.) is the main foliar constraint lowering yield. The objective of the study was to genetically improve grain yield and rust resistance of two locally adapted populations (Lam and Omoda), through two cycles of modified phenotypic S1 progeny recurrent selection. Treatments included three cycles of two locally adapted pearl millet populations, evaluated at three locations. Significant net genetic gain for grain yield (72 and 36%) were achieved in Lam and Omoda populations, respectively. This led to grain yield of 1,047 from 611 kg ha-1 in Lam population and 943 from 693 kg ha-1 in Omoda population. Significant improvement in rust resistance was achieved in the two populations, with a net genetic gain of -55 and -71% in Lam and Omoda populations, respectively. Rust severity reduced from 30 to 14% in Lam population and from 57 to 17% in Omoda population. Net positive genetic gains of 68 and 8% were also achieved for 1000-grain weight in Lam and Omoda, respectively. Traits with a net negative genetic gain in both populations were days to 50% flowering, days to 50% anthesis, days to 50% physiological maturity, flower-anthesis interval, plant height and leaf area.Dans la zones semi-arides en Ouganda, le milet perl\ue9 ( Pennisetum glaucum (L.) R. Br.) est principalement cultiv\ue9 comme culture vivri\ue8re et de rente, mais la maladie de rouille (Puccinia substriata var indica (L.) R. Br.) est la contrainte majeure affectant le rendement. L\u2019ojectif de l\u2019\ue9tude \ue9tait l\u2019am\ue9lioration du rendement en grains et la r\ue9sistance \ue0 la maladie de rouille chez deux populations localement adapt\ue9es milet perl\ue9 (Lam and Omoda), ceci \ue0 travers deux cycles de selection reccurente. Les traitements consistaient \ue0 trois cycles de deux populations localement adapt\ue9es de milet perl\ue9, \ue9valu\ue9es dans trois milieu diff\ue9rents. Un gain genetique significatif de 72 et 36% de rendements en grain a \ue9t\ue9 observe respectivement chez les populations de Lam et de Omoda. Ceci a occasionn\ue9 des rendements en grains de 1,047 kg ha-1 au lieu de 611 kg ha-1 chez la population de Lam et 943 kg ha-1 au lieu de 693 kg ha-1 chez la population de Omoda. Une am\ue9lioration significative de la r\ue9sistance \ue0 la maladie de rouille a \ue9t\ue9 obtenue au sein des deux populations, avec des gains g\ue9n\ue9tiques nets de -55 et -71% respectivement chez les populations de Lam et Omoda. La s\ue9v\ue9rit\ue9 de la maladie de rouille a \ue9t\ue9 de 30% \ue0 14% au sein de la population de Lam population et de 57% \ue0 17% au sein de la population de Omoda. Un gain g\ue9n\ue9tique positif net de 68 et 8% ont \ue9t\ue9 \ue9galement obtenu respectivement pour le poid de 1000 grains de Lam et 1000 de Omoda. Les caract\ue8res comme le nombre jours \ue0 50% de floraison, le nombre de jours \ue0 50% anth\ue8se, le nombre de jours \ue0 50% de maturit\ue9 physiologique, l\u2019intervalle de temps entre la floraison et l\u2019anth\ue8se, la hauteur des plants et la surface des feuilles

Exploiting Genetic Diversity for Adaptation and Mitigation of Climate Change: A Case of Finger Millet in East Africa

Eighty one finger millet germplasm accessions from East Africa were evaluated in eight environments in Kenya, Tanzania and Uganda for adaptation and grain yield stability, genotype and genotype x environment (GGE) models. Lanet 2012 long rains, Serere 2012 long rains and Miwaleni 2012 long rains were found to be the most discriminating environments for the low temperature, sub-humid mid-altitude and dry lowland areas, respectively. Seven genotypes were identifi ed for yield stability across the eight environments, whereas nine genotypes had specifi c adaptation. Fourteen genotypes attained the highest grain yield and had varied maturity, plant heights and grain colour. This will provide farmers the opportunity to select genotypes appropriate to their target agroecologies with desired traits. The East African fi nger millet germplasm has high potential as a source of climate smart, high yielding genotypes for direct production and/or breeding

Genetic diversity in East African finger millet (Eleusine coracana (L.) Gaertn) landraces based on SSR markers and some qualitative traits

In this study, genetic diversity in 340 finger millet accessions from Kenya, Tanzania and Uganda and 15 minicore accessions was assessed using 23 single-sequence repeat markers and five qualitative traits. Nineteen markers were polymorphic with a mean polymorphic information content value of 0.606 and a range of 0.035–0.889, with allele size ranging from 148 to 478. A total of 195 alleles were detected (range of 3–23 and average of 10.3 alleles per locus), with 57.7% being rare and 17.4% being private. Differentiation between the accessions of the three countries was weak, with most of the genetic diversity being explained by variability within the countries and subregions than by that among the countries and subregions. The highest genetic diversity was observed in the Kenyan accessions (0.638 ± 0.283) and the least in the Ugandan accessions (0.583 ± 0.264). The highest differentiation based on Wright's fixation index was observed between the Ugandan and Tanzanian accessions (F ST= 0.117; P< 0.001). There was no association between the morphological traits assessed and the genetic classes observed. The low variability between the countries could be attributed to a shared gene pool, as the crop originated from the East African region. Farmers' selection for adaptation and end use could have contributed to the high diversity within the countries. Concerted efforts need to be made to characterize the large germplasm stocks in East Africa for their effective conservation and utilization. The lack of representation of accessions from the three countries in all global minicore diversity clusters points to the need to explore the East African germplasm to identify the diversity not captured earlier to be included in the global repository

Exploiting Genetic Diversity for Adaptation and Mitigation of Climate Change: A Case of Finger Millet in East Africa

With the reality of global climate change there is a need to exploit the variation in the germplasm in order to develop genotypes adapted to these changes. This requires breeding and selection of crops at strategically selected locations along a rainfall/temperature gradient to enable farmers select desired cultivars. Eighty one finger millet germplasm lines from East Africa were evaluated in eight environments spread across Kenya, Tanzania and Uganda for adaptation, grain yield stability using the additive main effects and multiplicative interaction (AMMI) ANOVA and Genotype and Genotype x Environment (GGE) models and blast reaction under artificial and natural inoculation. Lanet 2012 long rains, Serere 2012 long rains and Miwaleni 2012 long rains were found to be the most discriminating environments for the low temperature, sub-humid mid-altitude and dry lowland areas, respectively. Alupe 2012 long rains was the ideal environment for blast selection. Seven genotypes were identified for yield stability across the eight environments whereas nine genotypes had specific adaptation. Nine genotypes were identified with resistance to three blast types. However, one and two genotypes had high resistance only to leaf and neck blast, respectively. Two resistant and 12 moderately resistant genotypes to blast attained the highest grain yields and had varied maturity, plant heights and grain colour. This will provide farmers the opportunity to select genotypes appropriate to their target agro-ecologies with desired end-uses. The East African finger millet germplasm has high potential as a source of climate smart high yielding and blast resistant genotypes for direct production and/or breeding

Genome-wide association study of root mealiness and other texture-associated traits in cassava

Open Access Journal; Published online: 17 Dec 2021Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low

Genetic diversity, population structure and inter-trait relationships of combined heat and drought tolerant early-maturing maize inbred lines from west and central Africa

Open Access Journal; Published online: 04 Sept 2020Adequate knowledge and understanding of the genetic diversity and inter-trait relationships among elite maize inbred lines are crucial for determining breeding strategies and predicting hybrid performance. The objectives of this study were to investigate the genetic diversity of 162 early maturing white and yellow tropical maize inbred lines, and to determine the population structure, heterotic groups and inter-trait relationships among the lines. Using 9684 DArT single nucleotide polymorphism (SNP) markers, a gene diversity (GD) of 0.30 was recorded for the inbred lines with polymorphic information content (PIC) ranging from 0.08 to 0.38. The genetic relatedness among the inbred lines evaluated revealed six different groups based on the history of selection, colour of endosperm and pedigree. The genotype-by-trait (GT) biplot analysis identified inbred 1 (TZEI 935) as outstanding in terms of combined heat and drought (HD) tolerance with the base index analysis identifying 15 superior inbreds in the HD environment. A wide range of genetic variability was observed among the inbred lines, indicating that they are an invaluable resource for breeding for HD tolerance in maize breeding programmes, especially in West and Central Africa