A single lycaenid caterpillar gets an ant‐constructed shelter and uninterrupted ant attendance

Ant‐lycaenid associations range from mutualism to parasitism and the caterpillars of some species of lycaenids are reported to enter ant nests for shelter, diapause, or pupation. The present study aimed to examine the nature of the association between Euchrysops cnejus (Fabricius) (Lepidoptera: Lycaenidae) and Camponotus compressus (Fabricius) (Hymenoptera: Formicidae) worker ants on the extrafloral nectary‐bearing cowpea plant, Vigna unguiculata (L.) Walp. (Fabaceae). The abundance patterns of the ants and the lycaenid caterpillars together with the spatial patrolling patterns of the ants on the plants revealed that ant abundance increased with the occurrence of the lycaenid caterpillars and the ants preferred the lycaenids over the extrafloral nectar. Camponotus compressus worker ants constructed a shelter at the cowpea plant base after interaction with one or more lycaenid caterpillar(s) and tended the caterpillars and pupae till the emergence of the butterfly. The ant‐constructed shelters (ACSs) inhabited by the minor caste workers (13 ± 1.3 ants per ACS), were utilized by the caterpillars to undergo pupation. The ants confined their activities predominantly to tending the pod‐feeding caterpillars and the solitary pupa within each ACS. It appears that the behavior of the tending worker ants is modulated by the lycaenid vulnerable stages.     

The genetics of domestication of yardlong bean, Vigna unguiculata (L.) Walp. ssp. unguiculata cv.-gr. sesquipedalis

Background and Aims

The genetics of domestication of yardlong bean [Vigna unguiculata (L.) Walp. ssp. unguiculata cv.-gr. sesquipedalis] is of particular interest because the genome of this legume has experienced divergent domestication. Initially, cowpea was domesticated from wild cowpea in Africa; in Asia a vegetable form of cowpea, yardlong bean, subsequently evolved from cowpea. Information on the genetics of domestication-related traits would be useful for yardlong bean and cowpea breeding programmes, as well as comparative genome study among members of the genus Vigna. The objectives of this study were to identify quantitative trait loci (QTLs) for domestication-related traits in yardlong bean and compare them with previously reported QTLs in closely related Vigna.

Methods

Two linkage maps were developed from BC₁F₁ and F₂ populations from the cross between yardlong bean (V. unguiculata ssp. unguiculata cv.-gr. sesquipedalis) accession JP81610 and wild cowpea (V. unguiculata ssp. unguiculata var. spontanea) accession TVnu457. Using these linkage maps, QTLs for 24 domestication-related traits were analysed and mapped. QTLs were detected for traits related to seed, pod, stem and leaf.

Key Results

Most traits were controlled by between one and 11 QTLs. QTLs for domestication-related traits show co-location on several narrow genomic regions on almost all linkage groups (LGs), but especially on LGs 3, 7, 8 and 11. Major QTLs for sizes of seed, pod, stem and leaf were principally located on LG7. Pleiotropy or close linkage of genes for the traits is suggested in these chromosome regions.

Conclusions

This is the first report of QTLs for domestication-related traits in yardlong bean. The results provide a foundation for marker-assisted selection of domestication-related QTLs in yardlong bean and enhance understanding of domestication in the genus Vigna.     

Genome resources for climate‐resilient cowpea,an essential crop for food security

Cowpea (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 crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K‐499‐35 include a whole‐genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi‐parental 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 SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new 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.     

Genomic dissection of pod shattering in common bean: mutations at non‐orthologous loci at the basis of convergent phenotypic evolution under domestication of leguminous species

The complete or partial loss of shattering ability occurred independently during the domestication of several crops. Therefore, the study of this trait can provide an understanding of the link between phenotypic and molecular convergent evolution. The genetic dissection of ‘pod shattering’ in Phaseolus vulgaris is achieved here using a population of introgression lines and next‐generation sequencing techniques. The ‘occurrence’ of the indehiscent phenotype (indehiscent versus dehiscent) depends on a major locus on chromosome 5. Furthermore, at least two additional genes are associated with the ‘level’ of shattering (number of shattering pods per plant: low versus high) and the ‘mode’ of shattering (non‐twisting versus twisting pods), with all of these loci contributing to the phenotype by epistatic interactions. Comparative mapping indicates that the major gene identified on common bean chromosome 5 corresponds to one of the four quantitative trait loci for pod shattering in Vigna unguiculata. None of the loci identified comprised genes that are homologs of the known shattering genes in Glycine max. Therefore, although convergent domestication can be determined by mutations at orthologous loci, this was only partially true for P. vulgaris and V. unguiculata, which are two phylogenetically closely related crop species, and this was not the case for the more distant P. vulgaris and G. max. Conversely, comparative mapping suggests that the convergent evolution of the indehiscent phenotype arose through mutations in different genes from the same underlying gene networks that are involved in secondary cell‐wall biosynthesis and lignin deposition patterning at the pod level.     

The parasitic fly Nemorilla maculosa exploits host‐plant volatiles to locate the legume pod borer,Maruca vitrata

Nemorilla maculosa Meigen (Diptera: Tachinidae) is a solitary endoparasitoid of the legume pod borer, Maruca vitrata Fabricius (Lepidoptera: Crambidae), a key pest of cowpea, Vigna unguiculata (L.) Walp. (Fabaceae) in Africa. A colony of N. maculosa, introduced for experimental purposes from Taiwan to the laboratories of the International Institute of Tropical Agriculture (IITA) in Benin, was used for our studies. Olfactory reponses of N. maculosa to leaves of infested or uninfested cowpea and yellow peabush, Sesbania cannabina (Retz.) Pers. (Fabaceae), and to M. vitrata larvae were evaluated in a four‐arm olfactometer. For all combinations of odor sources, responses between naïve and oviposition‐experienced female flies did not differ. Nemorilla maculosa females were attracted by odors from uninfested leaves of yellow peabush and flowers of cowpea when compared with clean air, and they were attracted to plants damaged by M. vitrata with larvae removed. However, the female fly did not discriminate between odors from infested and uninfested plants. The parasitic fly N. maculosa proved well able to use volatile compounds from various host plants (peabush and cowpea) to locate its host, with a more pronounced attraction by the combination of host larvae and infested host plant parts. These findings are discussed in light of the prospective use of N. maculosa as a biological control agent against the legume pod borer.     

Construction of a SSR-based genetic map and identification of QTL for domestication traits using recombinant inbred lines from a cross between wild and cultivated cowpea (<Emphasis Type="Italic">V. unguiculata</Emphasis> (L.) Walp.)

Cowpea (Vigna unguiculata (L.) Walp.) is a grain legume commonly grown and consumed in many parts of the tropics and subtropics. A genetic linkage map was constructed using simple sequence repeat (SSR) markers and a recombinant inbred (RI) population of159 individuals derived from a cross between the breeding line 524B, a California Blackeye, and 219-01, a perennial wild cowpea from Kenya. Out of 912 primer combinations predicted to amplify SSRs in cowpea, 639 reliably produced amplification products in PCR assays and 202 (31.6%) were polymorphic between the two parents. These polymorphic SSRs were used to construct a genetic map consisting of 11 linkage groups (LGs) spanning 677 cM, with an average distance between markers of 3 cM. Agronomic traits related to domestication (seed weight, pod shattering) were analyzed together with the genotypic data. Six quantitative trait loci (QTL) for seed size were revealed with the phenotypic variation ranging from 8.9 to 19.1%. Four QTL for pod shattering were identified with the phenotypic variation ranging from 6.4 to 17.2%. The QTL for seed size and pod shattering mainly cluster in two areas of LGs 1 and 10, facilitating the use of marker-assisted selection to eliminate undesirable wild phenotypes in breeding activities involving introgression of traits from wild germplasm. The generation of an SSR-based molecular map and additional trait-linked markers also contributes to the expanding tool kit available to cowpea breeders, especially in Africa.     

Regulation of Leaf Senescence by Reproductive Sink Intensity in Cowpea (Vigna unguiculata L. Walp)

The relationship between seed number per pod and senescenceof the leaf in its axil was examined in a determinate cowpea(Vigna unguiculata L. Walp) variety C.779. The seed number perpod was reduced at all fruiting nodes by surgical excision ofpart of the 4-d-old pod. Leaf senescence as measured by lossof leaf area, chlorophyll content and soluble protein was sloweddown in leaves supporting the development of an artificiallyreduced number of seeds. Diminished nitrogen mobilization fromthe leaf could not account for the reduced rate of leaf senescence.The result suggests the involvement of a senescence signal fromthe developing seeds to the leaf in its axil. Development ofthe basal half of the excised pod in the cowpea provides a uniquesystem for manipulating seed number per pod. Senescence, monocarpic, chlorophyll, protein, Vigna unguiculata, cowpea     

New resources for genetic studies in Populus nigra: genome‐wide SNP discovery and development of a 12k Infinium array

Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water‐use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead‐Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5–7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural‐population based genetic association studies in P. nigra.     

The genome of cowpea (Vigna unguiculata [L.] Walp.)

Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub‐Saharan Africa, that is resilient to hot and drought‐prone environments. An assembly of the single‐haplotype inbred genome of cowpea IT97K‐499‐35 was developed by exploiting the synergies between single‐molecule real‐time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination‐poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high‐recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS‐LRR and the SAUR‐like auxin superfamilies compared with other warm‐season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.     

Unusual Network of Internal Phloem in the Pod Mesocarp of Cowpea [Vigna unguiculata (L.) Walp. (Fabaceae)]

A mycelium-like network of internal phloem was observed in theinner mesocarp of the lateral pod walls of the fruit of certaingenotypes of cowpea [Vigna unguiculata (L.) Walp.] In the cultivarVita 3, the network consists of single, or rarely double, strandsof sieve elements and associated phloem parenchyma, orientedmainly parallel with the fibres of the adjacent endocarp, andstretching marginally beyond the sheets of fibres to connectabove and below with the outermost phloem of the longitudinalstrands of the dorsal and ventral sutures of the fruit. Theinternal phloem network does not relate conformationally to,or interconnect with the conventional (xylem+phloem) vasculatureof the mid mesocarp of the pod wall. In Vita 3, sieve elementsdifferentiate in the internal phloem after those in the majorveins of the pod, but before the presumptive endocarp fibrescommence wall thickening. The pod walls of twenty-one otherspecies of legumes proved negative for internal phloem, whileof nine varied genotypes of cowpea examined, six proved positive,three negative for the trait. Presence of internal phloem incowpea is not always associated with presence of endocarp fibresor necessarily with large fruits with large seeds. Possiblefunctions suggested for the phloem network are to provide assimilatesfor fibre wall thickening or to transport solutes to or fromsites of temporary storage in the fleshy inner layers of thepod wall. Internal phloem, legume fruit, translocation, mesocarp, pod wall, Vigna unguiculata, cowpea     

Influence of host use adaptation on the dispersal propensity of Callosobruchus maculatus

Local adaptation can lead to significant differences in host use that may influence population growth and spread. Here, we test the potential for adaptation of one behavioural component (host acceptance) to lead to cross‐adaptation for a separate behavioural component (dispersal propensity) using the cowpea seed beetle, Callosobruchus maculatus. C. maculatus originating from the same source population were subjected to selection for host use by rearing them for over 40 generations on either the preferred host of the ancestral population, Vigna radiata, or a marginal host for the ancestral population, Cicer arietinum. Host acceptance was then assayed using four choice and no‐choice oviposition assays including a low‐quality host, Lens culinaris, a marginal host, C. arietinum, and two high‐quality hosts, V. radiata and V. unguiculata. Dispersal was assayed in interconnected arenas containing one of three different hosts: V. radiata, V. unguiculata or C. arietinum. As expected, differences in host acceptance were present, in this case consisting of greater acceptance of the lower quality hosts in the C. arietinum population, but no significant differences in host preference hierarchy. Dispersal propensity in the C. arietinum population was significantly lower than in the V. radiata population, despite the absence of any difference in selection pressures for dispersal. Furthermore, significant differences in dispersal propensity in arenas containing different hosts were present in the V. radiata population, but not in the C. arietinum population. Results highlight the need to consider local adaptation when developing management recommendations, even for behaviours for which selection pressures are not directly apparent.     

Comprehensive genomic analyses of Vigna unguiculata provide insights into population differentiation and the genetic basis of key agricultural traits

Vigna unguiculata is an important legume crop worldwide. The subsp. sesquipedalis and unguiculata are the two major types grown; the former is mainly grown in Asia to produce fresh pods, while the latter is mainly grown in Africa to produce seeds. Here, a chromosome-scale genome for subsp. sesquipedalis was generated by combining high-fidelity (HiFi) long-read sequencing with high-throughput chromosome conformation capture (Hi-C) technology. The genome size for all contigs and N50 were 594 and 18.5 Mb, respectively. The Hi-C interaction map helped cluster 91% of the contigs into 11 chromosomes. Genome comparisons between subsp. sesquipedalis and unguiculata revealed extensive genomic variations, and some variations resulted in gene loss. A germplasm panel with 315 accessions of V. unguiculata was resequenced, and a genomic variation map was constructed. Population structure and phylogenetic analyses suggested that subsp. sesquipedalis originated from subsp. unguiculata. Highly differentiated genomic regions were also identified, and a number of genes functionally enriched in adaptations were located in these regions. Two traits, pod length (PL) and pod width (PW), were observed for this germplasm, and genome-wide association analysis of these traits was performed. The quantitative trait loci (QTLs) for these two traits were identified, and their candidate genes were uncovered. Interestingly, genomic regions of PL QTLs also showed strong signals of artificial selection. Taken together, the results of this study provide novel insights into the population differentiation and genetic basis of key agricultural traits in V. unguiculata.     

A multi‐parent advanced generation inter‐cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.)

Multi‐parent advanced generation inter‐cross (MAGIC) populations are an emerging type of resource for dissecting the genetic structure of traits and improving breeding populations. We developed a MAGIC population for cowpea (Vigna unguiculata L. Walp.) from eight founder parents. These founders were genetically diverse and carried many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in the United States and sub‐Saharan Africa, where cowpea is vitally important in the human diet and local economies. The eight parents were inter‐crossed using structured matings to ensure that the population would have balanced representation from each parent, followed by single‐seed descent, resulting in 305 F₈ recombinant inbred lines each carrying a mosaic of genome blocks contributed by all founders. This was confirmed by single nucleotide polymorphism genotyping with the Illumina Cowpea Consortium Array. These lines were on average 99.74% homozygous but also diverse in agronomic traits across environments. Quantitative trait loci (QTLs) were identified for several parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by biparental genetic mapping. The recombination events were concentrated in telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain, QTL and gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties.     

Active aggregation among sexes in bean flower thrips (Megalurothrips sjostedti) on cowpea (Vigna unguiculata)

Male sexual aggregations are a common territorial, mating‐related or resource‐based, behaviour observed in diverse organisms, including insects such as thrips. The influence of factors such as plant substrate, time of day, and geographic location on aggregation of thrips is uncertain, therefore we monitored the dispersion of male and female bean flower thrips (BFT), Megalurothrips sjostedti (Trybom) (Thysanoptera: Thripidae), on cowpea, Vigna unguiculata (L.) Walp. (Fabaceae), over three cowpea growth stages and across three cowpea‐growing areas of Kenya. Our results indicated that for all the crop growth stages, the density of BFTs varied over the time of day, with higher densities at 10:00, 13:00, and 16:00 hours than at 07:00 hours. Thrips densities did not differ among blocks at the budding stage, but they did at peak flowering and podding stages. Dispersion indices suggested that both male and female BFTs were aggregated. Active male aggregation occurred only on green plant parts and it varied across blocks, crop stages, and locations. Similarly, active female aggregation was observed in peak flowering and podding stages. Such active aggregation indicates a semiochemical or behaviour‐mediated aggregation. Identification of such a semiochemical may offer new opportunities for refining monitoring and management strategies for BFT on cowpea, the most important grain legume in sub‐Saharan Africa.     

CHLOROPLAST DNA POLYMORPHISM SUGGESTS NIGERIAN CENTER OF DOMESTICATION FOR THE COWPEA,VIGNA UNGUICULATA (LEGUMINOSAE)

Twenty-one independent chloroplast DNA polymorphisms were identified in Vigna unguiculata defining 19 different chloroplast DNA molecules (plastome types). Two plastome types, differing by a single character, were found among 32 accessions of cultivated cowpea (Vigna unguiculata ssp. unguiculata). Eighteen different plastome types were found among 26 accessions of wild cowpea (V. unguiculata ssp. dekindtiana). The very low level of chloroplast DNA diversity found in cultivated accessions relative to wild cowpea suggests that 1) the domesticated form was derived from a narrow selection of the wild germplasm and 2) chloroplast gene flow between wild and cultivated types has been very limited. Cladistic analysis of the cpDNA data generated a robust tree completely lacking homoplasy. Three wild accessions from Nigeria possessed a plastome type indistinguishable from one present in cultivated accessions, suggesting that Nigeria represents one center of domestication of the cowpea. The other plastome type within the cultivated germplasm was not found among wild accessions.     

Development and polymorphism of Vigna unguiculata ssp. unguiculata microsatellite markers used for phylogenetic analysis in asparagus bean (Vigna unguiculata ssp. sesquipedialis (L.) Verdc.)

Asparagus bean (V. unguiculata ssp. sesquipedialis), a specific form of cowpea (V. unguiculata L. Walp.), is cultivated as a vegetable crop throughout eastern and southern Asia for its tender long pods. Little is known about the genetic relationship between asparagus bean and the broader species, particularly the dominant ssp. unguiculata. We report here the development and transferability of simple sequence repeat (SSR) markers, over 40% of which are EST-derived, from ssp. unguiculata to asparagus bean and the use of a subset of the polymorphic markers to assess the genetic diversity of asparagus bean cultivars from diverse geographic origins across China. A total of 410 EST derived SSR (eSSR) markers and 600 SSR markers derived from cowpea genespace sequences (GSS) were developed, with a cross-subspecies transferability of 100% and 98.5%, respectively. In a recombinant inbred line population of asparagus bean, a 1:1 segregation was observed for most loci. Principal coordinate analysis (PCA) and phylogenetic clustering based on 62 alleles detected by 14 polymorphic SSR markers distinguished ssp. unguiculata and sesquipedialis into separate groups. Improved asparagus bean cultivars in China generally have a narrow genetic basis compared with landraces varieties. This suggests that asparagus bean breeding programs need to consider utilizing landrace germplasm to enhance genetic variability and ensure long-term gains from selection and reduce genetic vulnerability to pathogen/pest epidemics. Because of their transferability across subspecies, the SSR markers described in this study could be effectively employed in cross-subspecies trait introgression breeding from ssp. unguiculata to sesquipedialis.     

Binding of Vigna unguiculata vicilins to the peritrophic membrane of Tenebrio molitor affects larval development

We investigated the effects of vicilins (7S storage proteins) from Vigna unguiculata (L.) Walp. (Fabaceae), cultivars EPACE‐10 [genotype susceptible to the cowpea weevil, Callosobruchus maculatus (Fabricius)] and IT81D‐1045 [cowpea weevil‐resistant genotype], seeds on Tenebrio molitor L. (Coleoptera: Tenebrionidae) larval development. Toxicity of vicilins was investigated through the incorporation of these proteins in artificial diet offered to the larvae. Binding tests of vicilins to the peritrophic membranes (PM) were carried out by in vitro incubation of PM with solutions of vicilins. Bound proteins were desorbed from PM with 100 mm HCl. Desorbed vicilins were analyzed by sodium dodecyl sulfate–polyacrylamide gel electrophoresis followed by immunoprobing on Western blotting using an anti‐vicilin cv. EPACE‐10 antibody. The chitin content of the T. molitor PM was evaluated by the Von Wisselingh color test and presence of chitin in the larval PM was confirmed. Bioassays showed that both vicilins from EPACE‐10 and IT81D‐1045 genotypes were toxic to T. molitor larvae, and in vitro binding assays showed that these seed‐storage proteins were capable of binding to the larval PM.