scholarly journals Genome resources for climate-resilient cowpea, an essential crop for food security

2016 ◽  
Author(s):  
María Muñoz-Amatriaín ◽  
Hamid Mirebrahim ◽  
Pei Xu ◽  
Steve I. Wanamaker ◽  
MingCheng Luo ◽  
...  
Keyword(s):  
Food Security ◽  
Genetic Map ◽  
Physical Map ◽  
Primary Source ◽  
Artificial Chromosome ◽  
West African ◽  
Sub Saharan Africa ◽  
Breeding Lines ◽  
Security Issues ◽  
Legume Crop

SUMMARYCowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crop plants. Here we describe foundational genome resources and their application to analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include bacterial artificial chromosome (BAC) libraries and a BAC-based physical map, assembled sequences from 4,355 BACs, as well as a whole-genome shotgun (WGS) assembly. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for over 50,000 SNPs, which was then applied to five biparental RIL populations to produce a consensus genetic map containing 37,372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The genomes of West African breeding lines and landraces have regions of marked depletion of diversity, some of which coincide with QTL that may be the result of artificial selection or environmental adaptation. The new publicly available resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.

A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 32-37 ◽  
Author(s):  
Shoko Saji ◽  
Yosuke Umehara ◽  
Baltazar A Antonio ◽  
Hiroko Yamane ◽  
Hiroshi Tanoue ◽  
...  
Keyword(s):  
Genetic Map ◽  
Dna Markers ◽  
Yeast Artificial Chromosome ◽  
Physical Map ◽  
Genome Structure ◽  
Rice Genome ◽  
Artificial Chromosome ◽  
Physical Length ◽  
Rice Chromosomes ◽  
Yac Contig

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.Key words: physical mapping, YAC contig, rice genome, rice chromosomes.

Evaluation of cowpea (Vigna unguiculata (L.) Walp.) germplasm lines for tolerance to drought

2012 ◽  
Vol 10 (3) ◽  
pp. 171-176 ◽  
Author(s):  
Christian A. Fatokun ◽  
Ousmane Boukar ◽  
Satoru Muranaka
Keyword(s):  
Drought Tolerance ◽  
Sub Saharan Africa ◽  
Grain Legume ◽  
International Institute ◽  
Breeding Lines ◽  
Germplasm Collections ◽  
Legume Crop ◽  
Drought Tolerant ◽  
Cowpea Varieties ◽  
Sub Saharan

Cowpea is an important grain legume crop in sub-Saharan Africa (SSA) where, on a worldwide basis, the bulk is produced and consumed. The dry savanna area of SSA is where cowpea is mostly grown under rain-fed conditions. The crop is therefore prone to drought which may occur early, mid and/or late in the cropping season. Compared with many other crops, cowpea is drought tolerant, even though drought is still a major constraint limiting its productivity in SSA. Increasing the level of drought tolerance in existing cowpea varieties grown by farmers would enable them to obtain more and stable yield from their cowpea fields. As a first step towards enhancing drought tolerance in existing cowpea varieties, 1288 lines were selected randomly from cowpea germplasm collections maintained at the International Institute of Tropical Agriculture, and evaluated for their drought tolerance at Ibadan. Drought was imposed by withdrawal of irrigation from 5 weeks after sowing. On average, drought reduced the number of days to flower by 12 d, and the mean grain yield per plant was also reduced by 67.28%. A few of the cowpea lines stayed green for up to 6 weeks after irrigation was stopped, even though some of these produced no pods when the study was terminated. Further evaluation in the screenhouse of 142 selected drought-tolerant lines helped to identify six lines that could be potential parents for developing breeding lines with enhanced drought tolerance.

Bacterial artificial chromosome–based physical map of Gibberella zeae (Fusarium graminearum)

Genome ◽  
2007 ◽  
Vol 50 (10) ◽  
pp. 954-962 ◽  
Author(s):  
Yueh-Long Chang ◽  
Seungho Cho ◽  
H. Corby Kistler ◽  
Chun-Sheng Hsieh ◽  
Gary J. Muehlbauer
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Fusarium Graminearum ◽  
Genetic Map ◽  
Genome Sequence ◽  
Restriction Enzyme ◽  
Physical Map ◽  
Artificial Chromosome ◽  
Gibberella Zeae ◽  
Restriction Enzyme Site ◽  
Insert Size

Fusarium graminearum is the primary causal pathogen of Fusarium head blight of wheat and barley. To accelerate genomic analysis of F. graminearum, we developed a bacterial artificial chromosome (BAC)–based physical map and integrated it with the genome sequence and genetic map. One BAC library, developed in the HindIII restriction enzyme site, consists of 4608 clones with an insert size of approximately 107 kb and covers about 13.5 genome equivalents. The other library, developed in the BamHI restriction enzyme site, consists of 3072 clones with an insert size of approximately 95 kb and covers about 8.0 genome equivalents. We fingerprinted 2688 clones from the HindIII library and 1536 clones from the BamHI library and developed a physical map of F. graminearum consisting of 26 contigs covering 39.2 Mb. Comparison of our map with the F. graminearum genome sequence showed that the size of our physical map is equivalent to the 36.1 Mb of the genome sequence. We used 31 sequence-based genetic markers, randomly spaced throughout the genome, to integrate the physical map with the genetic map. We also end-sequenced 17 BamHI BAC clones and identified 4 clones that spanned gaps in the genome sequence. Our new integrated map is highly reliable and useful for a variety of genomics studies.

scholarly journals Adaptation of Grass Pea (Lathyrus sativus) to Mediterranean Environments

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1295 ◽  
Author(s):  
Diego Rubiales ◽  
Amero A. Emeran ◽  
Fernando Flores
Keyword(s):  
Grain Yield ◽  
Farming Systems ◽  
Field Testing ◽  
Sub Saharan Africa ◽  
Lathyrus Sativus ◽  
Limiting Factor ◽  
Grass Pea ◽  
Breeding Lines ◽  
Legume Crop ◽  
Ammi Analysis

Grass pea (Lathyrus sativus) is an annual legume crop widely cultivated in South Asia and Sub-Saharan Africa, but in regression in Mediterranean region. Its rusticity and nutritious value is calling back attention for its reintroduction into Mediterranean rain-fed farming systems. We studied the adaptation of a range of breeding lines in multi-environment field testing in Spain and Egypt, showing wide variation for grain yield. Broomrape (Orobanche crenata) infection appeared as the major limiting factor in both countries. Level of broomrape infection was highly influenced by environmental conditions, being favored by moderate temperatures at crop flowering and rain and humidity after flowering. The additive main effects and multiplicative interaction (AMMI) analysis was applied to understand the interaction between genotype (G) and environment (E) on grain yield and on broomrape infection. AMMI analyses revealed significant G and E effects as well as G*E interaction with respect to both traits. The AMMI analysis of variance (ANOVA) revealed that both, yield and broomrape infection were dominated by the environment main effect. AMMI1 biplot for grain yield revealed Ls10 and Ls11 as the accession with highest yields, closely followed by Ls16, Ls18 and Ls19. However, these accessions showed also lower stability, being particularly adapted to Delta Nile conditions. On the contrary, accessions Ls12 and Ls14 were more adapted to rain fed Spanish conditions. Accessions Ls7, Ls1 and Ls3 were the most stable over environments for grain yield.

scholarly journals Promoting Agricultural Research and Development to Strengthen Food Security in South Asia

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Ghose Bishwajit
Keyword(s):  
Food Security ◽  
Research And Development ◽  
South Asia ◽  
Agricultural Education ◽  
Agricultural Research ◽  
Sub Saharan Africa ◽  
Security Issues ◽  
Research And Innovation ◽  
Agricultural Research And Development ◽  
Sub Saharan

This study aims to highlight the status of agricultural R&D in South Asia and contends that creating an effective agricultural research and innovation systems is a vital element to ensure food security in this region. South Asia is home to around one-fourth of mankind and houses the largest proportion of undernourished people in the world. Despite a period of marked economic growth averaging 6% a year over the past two decades, it remains the world's second poorest region contributing a mere 2.2% in global annual GDP. Agriculture is the mainstay of South Asian economy employing around 60% of the total workforce and generating around 20% of total GDP. South Asia has the recognition of being the second most food-insecure region next only to sub-Saharan Africa. Though there is growing evidence that technological innovation has a key role to play in increasing agricultural production and strengthening food security, agricultural research and development (R&D) sector has failed to garner sufficient attention till now. This study also depicts the current situation of food security in South Asia and illustrates how agricultural education and innovation hold the master key to solve the food security issues for the world's most densely populated region.

scholarly journals Heterogeneity in Rates of Recombination Across the Mouse Genome

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 537-548 ◽  
Author(s):  
Michael W Nachman ◽  
Gary A Churchill
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Large Scale ◽  
Physical Map ◽  
Genetic Maps ◽  
Recombination Rates ◽  
Physical Maps ◽  
Genomic Patterns ◽  
Mary Lyon ◽  
Microsatellite Linkage

Abstract If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.

High Frequency Recombination During the Sexual Cycle of Dictyostelium discoideum

Genetics ◽  
1998 ◽  
Vol 148 (4) ◽  
pp. 1829-1832 ◽  
Author(s):  
David Francis
Keyword(s):  
Dictyostelium Discoideum ◽  
Genetic Map ◽  
High Frequency ◽  
Cell Biology ◽  
Physical Map ◽  
Genetic System ◽  
Sexual Cycle ◽  
Chromosome 2 ◽  
New Combinations ◽  
Restriction Sites

Abstract Analysis of Dictyostelium development and cell biology has suffered from the lack of an ordinary genetic system whereby genes can be arranged in new combinations. Genetic exchange between two long ignored strains, A2Cycr and WS205 is here reexamined. Alleles which differ in size or restriction sites between these two strains were found for seven genes. Six of these are in two clusters on chromosome 2. Frequencies of recombinant progeny indicate that the genetic map of the two mating strains is colinear with the physical map recently worked out for the standard nonsexual strain, NC4. The rate of recombination is high, about 0.1% per kilobase in three different regions of chromosome 2. This value is comparable to rates found in yeast, and will permit fine dissection of the genome.

scholarly journals An Ecosystem-Based Approach to Climate-Smart Agriculture with Some Considerations for Social Equity

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1564
Author(s):  
Kofi Akamani
Keyword(s):  
Climate Change ◽  
Food Security ◽  
Ecosystem Management ◽  
Social Equity ◽  
Sub Saharan Africa ◽  
Management Approach ◽  
Agricultural System ◽  
Illustrative Case ◽  
Mitigation And Adaptation ◽  
Smart Agriculture

Although the transition to industrial agriculture in the 20th century resulted in increased agricultural productivity and efficiency, the attainment of global food security continues to be elusive. Current and anticipated impacts of climate change on the agricultural sector are likely to exacerbate the incidence of food insecurity. In recent years, climate-smart agriculture has gained recognition as a mechanism that has the potential to contribute to the attainment of food security and also enhance climate change mitigation and adaptation. However, several conceptual and implementation shortfalls have limited the widespread adoption of this innovative agricultural system at the landscape scale. This manuscript argues for the use of ecosystem management as an overarching framework for the conceptualization and implementation of climate-smart agriculture. The manuscript focuses on clarifying the foundational assumptions and management goals, as well as the knowledge and institutional requirements of climate-smart agriculture using the principles of ecosystem management. Potential challenges that may be faced by the application of an ecosystem management approach to climate-smart agriculture are also discussed. Furthermore, the manuscript calls for a heightened focus on social equity in the transition toward an ecosystem-based approach to climate-smart agriculture. The US farm bill is used as an illustrative case study along with other examples drawn mostly from sub-Saharan Africa.

scholarly journals Is High Whitefly Abundance on Cassava in Sub-Saharan Africa Driven by Biological Traits of a Specific, Cryptic Bemisia tabaci Species?

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 260
Author(s):  
Habibu Mugerwa ◽  
Peter Sseruwagi ◽  
John Colvin ◽  
Susan Seal
Keyword(s):  
Food Security ◽  
Bemisia Tabaci ◽  
Development Time ◽  
Adult Emergence ◽  
Sub Saharan Africa ◽  
Biological Traits ◽  
Population Development ◽  
Species Classification ◽  
First Instar ◽  
Sub Saharan

In East Africa, the prevalent Bemisia tabaci whiteflies on the food security crop cassava are classified as sub-Saharan Africa (SSA) species. Economically damaging cassava whitefly populations were associated with the SSA2 species in the 1990s, but more recently, it has been to SSA1 species. To investigate whether biological traits (number of first instar nymphs, emerged adults, proportion of females in progeny and development time) of the cassava whitefly species are significant drivers of the observed field abundance, our study determined the development of SSA1 sub-group (SG) 1 (5 populations), SG2 (5 populations), SG3 (1 population) and SSA2 (1 population) on cassava and eggplant under laboratory conditions. SSA1-(SG1-SG2) and SSA2 populations’ development traits were similar. Regardless of the host plant, SSA1-SG2 populations had the highest number of first instar nymphs (60.6 ± 3.4) and emerged adults (50.9 ± 3.6), followed by SSA1-SG1 (55.5 ± 3.2 and 44.6 ± 3.3), SSA2 (45.8 ± 5.7 and 32.6 ± 5.1) and the lowest were SSA1-SG3 (34.2 ± 6.1 and 32.0 ± 7.1) populations. SSA1-SG3 population had the shortest egg–adult emergence development time (26.7 days), followed by SSA1-SG1 (29.1 days), SSA1-SG2 (29.6 days) and SSA2 (32.2 days). Regardless of the whitefly population, development time was significantly shorter on eggplant (25.1 ± 0.9 days) than cassava (34.6 ± 1.0 days). These results support that SSA1-(SG1-SG2) and SSA2 B. tabaci can become highly abundant on cassava, with their species classification alone not correlating with observed abundance and prevalence.

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