Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.

Open Access Journal; Published online: 23 Feb. 2017White clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. The aim of this work was to characterize its molecular response to water deficit and recovery following re-hydration to identify targets for the breeding of tolerant varieties. We created a white clover reference transcriptome of 16,193 contigs by deep sequencing (mean base coverage 387x) four Suppression Subtractive Hybridization (SSH) libraries (a forward and a reverse library for each treatment) constructed from young leaf tissue of white clover at the onset of the response to drought and recovery. Reads from individual libraries were then mapped to the reference transcriptome and processed comparing expression level data. The pipeline generated four robust sets of transcripts induced and repressed in the leaves of plants subjected to water deficit stress (6,937 and 3,142, respectively) and following re-hydration (6,695 and 4,897, respectively). Semi-quantitative polymerase chain reaction was used to verify the expression pattern of 16 genes. The differentially expressed transcripts were functionally annotated and mapped to biological processes and pathways. In agreement with similar studies in other crops, the majority of transcripts up-regulated in response to drought belonged to metabolic processes, such as amino acid, carbohydrate, and lipid metabolism, while transcripts involved in photosynthesis, such as components of the photosystem and the biosynthesis of photosynthetic pigments, were up-regulated during recovery. The data also highlighted the role of raffinose family oligosaccharides (RFOs) and the possible delayed response of the flavonoid pathways in the initial response of white clover to water withdrawal. The work presented in this paper is to our knowledge the first large scale molecular analysis of the white clover response to drought stress and re-hydration. The data generated provide a valuable genomic resource for marker discovery and ultimately for the improvement of white clover

MECHANISM FOR POLLINATION IN AFRICAN YAM BEAN

African yam bean (AYB) ( Sphenostylis stenocarpa (Hochst Ex. A. Rich) Harms is a neglected and underutilised legume in tropical Africa. Its utilisation has been hampered by the presence of anti-nutritional factors and lack of improved varieties. The objective of this study was to investigate pollination and determine the rates of selfing and outcrossing in the species. Accession TSs5 had the highest fruit set (63.16%) in the open-pollinated breeding method; while AYB50 had the lowest value (46.61%). Seed set in the selfed accessions ranged from 91.45% (AYB50) to 94.97% (TSs66). Fruit set was highest in the open-pollinated breeding method, with a mean average fruit set of 51.32%. Significant differences (P < 0.01) were obtained in fruit set from accessions isolated with net bags which had the lowest seed set (88.91%) Seed set was highest (92.92%) in the selfed accessions. The self incompatibility index ranged from 1.33 to 2.26 and the rate of fruit set from artificial self-pollination was greater than 30% in the field, and the screen house showing that the species is highly self compatible. Selfing and outcrossing rates of 91.38 and 8.62% showed that S. stenocarpa is not an obligate selfer. AYB sets fruits and seeds when open pollinated, isolated, selfed or crossed with other accessions.La l\ue9gumineuse igname de l\u2019Afrique (AYB) ( Sphenostylis stenocarpa (Hochst Ex. A. Rich) Harms est une l\ue9gumineuse n\ue9glig\ue9e et sous utilis\ue9e en Afrique tropicale. Sa teneur en substances toxique et le manque de vari\ue9t\ue9s am\ue9lior\ue9es constituent un frein pour son utilisation massive. Il a \ue9t\ue9 ici question d\u2019\ue9tudier sa pollinisation et de d\ue9terminer les taux de pollinisation crois\ue9e et auto-pollinisation dans l\u2019esp\ue9ce. L\u2019accession TSs5 avait le nombre de gousses le plus \ue9lev\ue9 (63,16%) sous pollinisation ouverte, tandis que l\u2019accession AYB50 a exhib\ue9 la valeur la plus faible (46,61%). Les nombres de gousses sous auto pollinisation variaient de 91,45% (AYB50) \ue0 94,97% (TSs66). Ce nombre \ue9tait plus \ue9lev\ue9 sous pollinisation ouverte, avec une moyenne de 51,32%. Des differences significatives (P < 0.01) ont \ue9t\ue9 observ\ue9es dans les nombres de gousses chez les accessions prot\ue9g\ue9es par des filets et qui avaient les plus faibles nombres de grains (88,91%). Le nombre de grains le plus \ue9lev\ue9 (92,92%) \ue9tait observ\ue9 par auto pollinisation. L\u2019indice de d\u2019auto incompatibilit\ue9 \ue9tait de 1,33 \ue0 2,26 et le taux de fructification chez les plantes artificiellement auto pollinis\ue9es \ue9tait sup\ue9rieur \ue0 30% dans le champs, et en serre, indiquant ainsi que l\u2019esp\ue8ce est hautement auto compatible. Les taux d\u2019auto pollinisation 91,38 et de pollinisation crois\ue9e 8,62% montrent que l\u2019auto pollinisation chez S. stenocarpa n\u2019est pas obligatoire. AYB produit des gousses et graines sous toutes forms de pollinisation

Further evidence that the Genebank standards for drying orthodox seeds may not be optimal for subsequent seed longevity

Open Access ArticleMaximizing seed longevity is important for genebanks to efficiently manage their accessions, reducing the frequency of costly regeneration cycles and the loss of genetic integrity. Research on rice seeds has shown that subsequent longevity in air-dry storage can be improved by drying seeds, which are metabolically active at harvest (moisture contents above a critical value close to 16.5%), for an initial period at a higher temperature (40°C–60°C) than that currently recommended by the current genebank standards (5°C–20°C). The aim of this study was to test whether similar benefits could be achieved in two legume species—cowpea and soya bean—by drying freshly harvested seeds, from two separate harvests, at 40°C and 35% relative humidity, for up to 8 days before equilibrium drying in a drying room (17°C and 15% relative humidity). Improvements in longevity were observed in three of the four accessions of soya bean, with the greatest improvement generally occurring after the maximum duration (8 days) at the higher temperature. However, of the five accessions of cowpea, only seeds of TVu-9698 and TVu-13209 from the first harvest, and of TVu-13193 from the second harvest, showed an improvement in longevity compared with drying following the standard protocol. A negative effect of high-temperature drying was also observed in one accession of cowpea, TVu-11980, but only in seeds harvested later in the season, 13 weeks after planting. This research not only provides evidence of the potential benefits of drying orthodox seeds at an alternative, higher, temperature instead of at the conventional lower temperature, before long-term storage, but also raises awareness of how genebanks can improve the management of their accessions

Nutrient and antinutrient composition of winged bean (Psophocarpus tetragonolobus (L.) DC.) seeds and tubers

Open Access Journal; Published online: 03 Oct 2019Many people in sub-Saharan Africa suffer from protein malnutrition; this results in negative health and economic impacts. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is a tropical underutilized legume with beneficial nutritional characteristics such as high protein content, which may help to alleviate these problems. The proximate composition (fat, moisture content, crude protein, ash, and carbohydrate) and antinutrient (tannin and phytate) level of winged bean seeds and tubers were determined using 50 accessions. In the processed seeds, accession Tpt17 had the highest protein content (40.30%) and Tpt48 the lowest (34.18%). In the unprocessed seeds, Tpt17 also recorded the highest crude protein (31.13%) with Tpt125 having the lowest (28.43%). In the tubers, protein content ranged from 19.07% (Tpt42) to 12.26% (Tpt10). The moisture content in the processed seeds ranged from 8.51% (Tpt42) to 6.72% (Tpt6); in the unprocessed seeds, it was between 8.53% (Tpt53) and 3.76% (Tpt14). In the processed seeds, the values of ash ranged from 4.93% (Tpt126) to 4.45% (Tpt15-4); in the unprocessed seeds, it ranged from 4.98% (Tpt17) to 4.55% (Tpt125). In the processed seeds, the fat content ranged from 18.91% (Tpt51) to 14.09% (Tp43) while in the unprocessed seeds, the values ranged from 19.01% (Tpt15) to 13.87% (Tpt3-B). The crude fiber in the processed samples ranged from 13.82% (Tpt6) to 10.40% (Tpt125) while in the unprocessed seeds, it ranged from 7.29% in Tpt51 to 4.83% in Tpt11. Carbohydrate content in the processed seeds ranged from 26.30% (Tpt3-B) to 20.94% (Tpt125) and 39.76% in Tpt3-B to 34.53% in Tpt18 in the unprocessed seeds. The tannin and phytate contents showed remarkably significant differences. In the tubers harvested, significant variation was observed in the parameters evaluated. Winged bean flour could be formulated into various meals for children and adults to reduce malnutrition in sub-Saharan Africa

Genetic diversity and population structure of a mini-core subset from the world cowpea (Vigna unguiculata (L.) Walp.) germplasm collection

Open Access Journal; Published online: 30 Oct 2018The International Institute of Tropical Agriculture maintains the world’s largest collection of cowpea germplasm of over 15,000 accessions. A sub-set of 298 lines from the loosely composed mini core collection of 370 landraces were genotyped based on genotyping by sequencing (GBS). Ward’s minimum variance hierarchical cluster analysis, model-based ancestry analysis and discriminant analysis of principal component (DAPC) were carried out on this sub-set. Three clusters were identified by the different clustering methods. Principal component analysis further supported the three clusters especially when accessions are scattered along the axes of the first two principal components. The first two principal components explained a total of 22.30% of the variation. Cluster one comprises 115 accessions from the largest number of countries and has the highest gene diversity, heterozygosity and polymorphic information content (PIC) values. Cluster two is made up of 102 accessions, 90 percent of which are from West and Central Africa. Analysis of molecular variance shows that the most variation is among accessions and lowest among clusters. No cluster is made exclusively of accessions from a single country. Based on SNP markers, the sub set of cowpea mini core germplasm collection used in this study encompasses the diversity in the crop

Application of genomicsassisted breeding for generation of climate resilient crops: progress and prospects

CCAFS Climat

Navigating the international exchange of plant genetic resources amidst biosecurity challenges: experiences of IITA in Africa

Article in Pres

Antioxidant activity and acetylcholinesterase inhibition of field and in vitro grown Musa L. species

Published online: 12 October 2016Bananas and plantains (Musa L. species) have medicinal applications against diseases such as hypoglycemia, hypertension, and neurological disorders, especially Alzheimer’s disease. The demand for these plants is growing very fast, resulting in a relatively heavy load on Musaceae genetic resources. The study evaluated and compared the acetylcholinesterase (AChE) inhibition and antioxidant activity of field and in vitro plant materials of nine accessions of Musa spp. consisting of Tropical Musa banana (TMb: TMb 106, TMb 145, TMb 8, TMb 82, TMb 55) and Tropical Musa plantain (TMp: TMp 116, TMp 24, TMp 36) from the International Institute of Tropical Agriculture and Musa sapientum (MS) from the University of Ibadan Botanical garden, Nigeria. Musa accessions were estimated onto Murashige and Skoog (MS) medium supplemented with 0.18 mg/L indole acetic acid (IAA) and 4.5 mg/L benzyl amino purine (BAP). The in vitro grown accessions behaved differently with TMb 8 having the highest average shoot length of 5.03 ± 0.66 cm, and average number of leaves of 5.65 ± 0.38 cm at the end of 6 weeks. Leaf extracts provide more quantity of phenolics, flavonoids and higher 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity than the fruit extracts. The AChEI activity of the field plants ranged from 60.54 ± 0.54 to 98.46 ± 0.09 % and in vitro plants from 61.88 ± 0.11 to 76.60 ± 0.34 % at 200 µg/mL. Crude methanol extract (CME) of the in vitro plants showed higher DPPH antioxidant activity than the field plants with IC50 (extract concentration providing 50 % inhibition) values ranging from 9.57 ± 0.24 to 48.37 ± 0.62 µg/mL compared with CME of the field samples, which had IC50 ranging from 75.86 ± 1.76 to 162.20 ± 3.77 µg/mL. Plant tissue culture can be a reliable alternative cultivation method for mass propagation and conservation of Musa species for the production of antioxidant and acetylcholinesterase metabolites

Analysis of genetic diversity of African yam bean using SSR markers derived from cowpea

African yam bean, AYB (Sphenostylis stenocarpa Hochst. ex. A. Rich Harms), is a tuberous legume of tropical Africa. AYB has the potential to significantly boost food security due to its considerable nutritional qualities. However, the crop is underutilized. To efficiently utilize AYB genetic resources for its improvement, it is necessary to understand the crop’s diversity. This study investigated the amplification ability of 36 cowpea simple sequence repeat (SSR) primers across AYB genomic DNA, extracted from 67 accessions. Thirteen (36%) of the cowpea SSRs showed transferability in AYB. Eight of these SSRs amplified above 60% of AYB accessions and generated 55 polymorphic fragments with an average of 6.9 per primer. Polymorphic information content ranged from 0.6691 to 0.8857 with an average of 0.7791. This study also assessed the genetic diversity within 67 AYB accessions using eight cowpea (Vigna unguiculata L. Walp)-derived SSR primers. The result revealed a high level of genetic diversity with simple matching coefficient ranging from 0.458 to 1.000. A dendrogram depicting three main clusters was generated based on unweighted pair group method with arithmetic average. Cluster 1 was the most diverse with a dissimilarity range of 0.517–1.000. The level of genetic diversity revealed in this study indicates that the studied AYB germplasm can be exploited for genetic improvement. Additionally, the transferable markers will aid AYB genome research and also make possible the comparative mapping between AYB and cowpea.African yam bean, AYB (Sphenostylis stenocarpa Hochst. ex. A. Rich Harms), is a tuberous legume of tropical Africa. AYB has the potential to significantly boost food security due to its considerable nutritional qualities. However, the crop is underutilized. To efficiently utilize AYB genetic resources for its improvement, it is necessary to understand the crop’s diversity. This study investigated the amplification ability of 36 cowpea simple sequence repeat (SSR) primers across AYB genomic DNA, extracted from 67 accessions. Thirteen (36%) of the cowpea SSRs showed transferability in AYB. Eight of these SSRs amplified above 60% of AYB accessions and generated 55 polymorphic fragments with an average of 6.9 per primer. Polymorphic information content ranged from 0.6691 to 0.8857 with an average of 0.7791. This study also assessed the genetic diversity within 67 AYB accessions using eight cowpea (Vigna unguiculata L. Walp)-derived SSR primers. The result revealed a high level of genetic diversity with simple matching coefficient ranging from 0.458 to 1.000. A dendrogram depicting three main clusters was generated based on unweighted pair group method with arithmetic average. Cluster 1 was the most diverse with a dissimilarity range of 0.517–1.000. The level of genetic diversity revealed in this study indicates that the studied AYB germplasm can be exploited for genetic improvement. Additionally, the transferable markers will aid AYB genome research and also make possible the comparative mapping between AYB and cowpea.African yam bean, AYB (Sphenostylis stenocarpa Hochst. ex. A. Rich Harms), is a tuberous legume of tropical Africa. AYB has the potential to significantly boost food security due to its considerable nutritional qualities. However, the crop is underutilized. To efficiently utilize AYB genetic resources for its improvement, it is necessary to understand the crop’s diversity. This study investigated the amplification ability of 36 cowpea simple sequence repeat (SSR) primers across AYB genomic DNA, extracted from 67 accessions. Thirteen (36%) of the cowpea SSRs showed transferability in AYB. Eight of these SSRs amplified above 60% of AYB accessions and generated 55 polymorphic fragments with an average of 6.9 per primer. Polymorphic information content ranged from 0.6691 to 0.8857 with an average of 0.7791. This study also assessed the genetic diversity within 67 AYB accessions using eight cowpea (Vigna unguiculata L. Walp)-derived SSR primers. The result revealed a high level of genetic diversity with simple matching coefficient ranging from 0.458 to 1.000. A dendrogram depicting three main clusters was generated based on unweighted pair group method with arithmetic average. Cluster 1 was the most diverse with a dissimilarity range of 0.517–1.000. The level of genetic diversity revealed in this study indicates that the studied AYB germplasm can be exploited for genetic improvement. Additionally, the transferable markers will aid AYB genome research and also make possible the comparative mapping between AYB and cowpea.African yam bean, AYB (Sphenostylis stenocarpa Hochst. ex. A. Rich Harms), is a tuberous legume of tropical Africa. AYB has the potential to significantly boost food security due to its considerable nutritional qualities. However, the crop is underutilized. To efficiently utilize AYB genetic resources for its improvement, it is necessary to understand the crop’s diversity. This study investigated the amplification ability of 36 cowpea simple sequence repeat (SSR) primers across AYB genomic DNA, extracted from 67 accessions. Thirteen (36%) of the cowpea SSRs showed transferability in AYB. Eight of these SSRs amplified above 60% of AYB accessions and generated 55 polymorphic fragments with an average of 6.9 per primer. Polymorphic information content ranged from 0.6691 to 0.8857 with an average of 0.7791. This study also assessed the genetic diversity within 67 AYB accessions using eight cowpea (Vigna unguiculata L. Walp)-derived SSR primers. The result revealed a high level of genetic diversity with simple matching coefficient ranging from 0.458 to 1.000. A dendrogram depicting three main clusters was generated based on unweighted pair group method with arithmetic average. Cluster 1 was the most diverse with a dissimilarity range of 0.517–1.000. The level of genetic diversity revealed in this study indicates that the studied AYB germplasm can be exploited for genetic improvement. Additionally, the transferable markers will aid AYB genome research and also make possible the comparative mapping between AYB and cowpea