Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.)

The pattern of genetic variability in a core collection of 2,021 cowpea accessions

Cowpea is a highly drought-adapted leguminous crop with great promise for improving agricultural sustainability and food security. Here, we report analyses derived from array-based genotyping of 2,021 accessions constituting a core subset of the world's largest cowpea collection, held at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. We used this dataset to examine genetic variation and population structure in worldwide cowpea. We confirm that the primary pattern of population structure is two geographically defined subpopulations originating in West and East Africa, respectively, and that population structure is associated with shifts in phenotypic distribution. Furthermore, we establish the cowpea core collection as a resource for genome-wide association studies by mapping the genetic basis of several phenotypes, with a focus on seed coat pigmentation patterning and color. We anticipate that the genotyped IITA Cowpea Core Collection will serve as a powerful tool for mapping complex traits, facilitating the acceleration of breeding programs to enhance the resilience of this crop in the face of rapid global climate change.

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.

Rapid genomic evolution in Brassica rapa with bumblebee selection in experimental evolution

BACKGROUND

Insect pollinators shape rapid phenotypic evolution of traits related to floral attractiveness and plant reproductive success. However, the underlying genomic changes remain largely unknown despite their importance in predicting adaptive responses to natural or to artificial selection. Based on a nine-generation experimental evolution study with fast cycling Brassica rapa plants adapting to bumblebees, we investigate the genomic evolution associated with the previously observed parallel phenotypic evolution. In this current evolve and resequencing (E&R) study, we conduct a genomic scan of the allele frequency changes along the genome in bumblebee-pollinated and hand-pollinated plants and perform a genomic principal component analysis (PCA).

RESULTS

We highlight rapid genomic evolution associated with the observed phenotypic evolution mediated by bumblebees. Controlling for genetic drift, we observe significant changes in allelic frequencies at multiple loci. However, this pattern differs according to the replicate of bumblebee-pollinated plants, suggesting putative non-parallel genomic evolution. Finally, our study underlines an increase in genomic variance implying the putative involvement of multiple loci in short-term pollinator adaptation.

CONCLUSIONS

Overall, our study enhances our understanding of the complex interactions between pollinator and plants, providing a stepping stone towards unravelling the genetic basis of plant genomic adaptation to biotic factors in the environment.

Field assessment of yield and its contributing traits in cowpea treated with lower, intermediate, and higher doses of gamma rays and sodium azide

Across the globe, plant breeders of different organizations are working in collaboration to bring preferred traits to crops of economic importance. Among the traits, "high yielding potential" is the most important as it is directly associated with food security and nutrition, one of the sustainable development goals. The Food and Agriculture Organization acknowledges plant breeders' role and efforts in achieving local and global food security and nutrition. Recognizing the importance of pulses and increasing pressure on food security, the United Nations General Assembly declared 2016 the "International year of Pulses" owing to their preferred traits such as climate change resilience, wide adaptability, low agriculture input, and protein- and nutrient-rich crops. Keeping all these developments in consideration, we initiated an induced mutagenesis program by treating cowpea (Vigna unguiculata L. Walp.) with different doses of gamma rays and sodium azide aiming to enhance the yielding potential of an otherwise outstanding variety viz., Gomati VU-89 and Pusa-578. We noticed a substantial increase in mean values of agronomic traits in putative mutants raised from seeds treated with lower and intermediate doses of mutagens. Statistical analysis such as correlation, path, hierarchical clustering analysis (HCA), and principal component analysis (PCA) were used to assess the difference between mutagenized and control populations. A significant and positive correlation of yield with yield-attributing traits was recorded. However, among all the yield attributing traits, seeds per pod (SPP) depicted the maximum direct impact upon yield, and therefore, working on this trait may yield better results. A widely used PCA revealed 40.46% and 33.47% of the total variation for var. Gomati VU-89 and var. Pusa-578, respectively. Cluster analysis clustered treated and control populations into separate clusters with variable cluster sizes. Cluster V in the variety Gomati VU-89 and cluster V and VI in the variety Pusa 578 comprised of putative mutants were higher yielding and hence could be recommended for selection in future breeding programs. We expect to release such mutant lines for farmer cultivation in Northern parts of India depending on the performance of such high-yielding mutant lines at multilocations.

Walnut N-Acetylserotonin Methyltransferase Gene Family Genome-Wide Identification and Diverse Functions Characterization During Flower Bud Development

Melatonin widely mediates multiple developmental dynamics in plants as a vital growth stimulator, stress protector, and developmental regulator. N-acetylserotonin methyltransferase (ASMT) is the key enzyme that catalyzes the final step of melatonin biosynthesis in plants and plays an essential role in the plant melatonin regulatory network. Studies of ASMT have contributed to understanding the mechanism of melatonin biosynthesis in plants. However, AMST gene is currently uncharacterized in most plants. In this study, we characterized the JrASMT gene family using bioinformatics in a melatonin-rich plant, walnut. Phylogenetic, gene structure, conserved motifs, promoter elements, interacting proteins and miRNA analyses were also performed. The expansion and differentiation of the ASMT family occurred before the onset of the plant terrestrialization. ASMT genes were more differentiated in dicotyledonous plants. Forty-six ASMT genes were distributed in clusters on 10 chromosomes of walnut. Four JrASMT genes had homologous relationships both within walnut and between species. Cis-regulatory elements showed that JrASMT was mainly induced by light and hormones, and targeted cleavage of miRNA172 and miR399 may be an important pathway to suppress JrASMT expression. Transcriptome data showed that 13 JrASMT were differentially expressed at different periods of walnut bud development. WGCNA showed that JrASMT1/10/13/23 were coexpressed with genes regulating cell fate and epigenetic modifications during early physiological differentiation of walnut female flower buds. JrASMT12/28/37/40 were highly expressed during morphological differentiation of flower buds, associated with altered stress capacity of walnut flower buds, and predicted to be involved in the regulatory network of abscisic acid, salicylic acid, and cytokinin in walnut. The qRT-PCR validated the results of differential expression analysis and further provided three JrASMT genes with different expression profiles in walnut flower bud development. Our study explored the evolutionary relationships of the plant ASMT gene family and the functional characteristics of walnut JrASMT. It provides a valuable perspective for further understanding the complex melatonin mechanisms in plant developmental regulation.

Genetic differentiation of grain, fodder and pod vegetable type cowpeas (Vigna unguiculata L.) identified through single nucleotide polymorphisms from genotyping-by-sequencing

The species Vigna unguiculata L. (Walp), commonly known as cowpea, is a multi-purpose legume that has been selected into three subspecies that are divided into grain, fodder and pod (yardlong bean) types. However, genetic bases for distinctions are not well understood. The purpose of this study was to apply genotyping-by-sequencing (GBS) and current reference genome for V. unguiculata to distinguish three subspecies and identify signatures of divergence. The collection of 130 accessions included 128 cultivated from: 1) ssp. cylindrica, fodder type; 2) ssp. sesquipedalis, pod vegetable type; and 3) ssp. unguiculata, grain type. Two wilds genotypes from spp. dekindtiana and spp. pubescens, were used to anchor phylogeny. A total of 11,083 highly informative single nucleotide polymorphisms (SNPs) were discovered. Wild accessions showed distinct genetic fingerprints and were separated from cultivated subspecies. Principal component analysis showed closer relationship between ssp. unguiculata and ssp. cylindrica compared to ssp. sesquipedalis. Relative differentiation of cultivated subspecies (with Fixation Index, FST) indicated the existence of discrete signatures of selection. This work clarifies the population structure, phylogeny, and domestication of cultivated cowpeas. Furthermore, significant genetic differences between grain and pod vegetable types can provide valuable information for future breeding in three cowpea groups.

Revisiting the Domestication Process of African Vigna Species (Fabaceae): Background, Perspectives and Challenges

Legumes are one of the most economically important and biodiverse families in plants recognised as the basis to develop functional foods. Among these, the Vigna genus stands out as a good representative because of its relatively recent African origin as well as its outstanding potential. Africa is a great biodiversity centre in which a great number of species are spread, but only three of them, Vigna unguiculata, Vigna subterranea and Vigna vexillata, were successfully domesticated. This review aims at analysing and valorising these species by considering the perspective of human activity and what effects it exerts. For each species, we revised the origin history and gave a focus on where, when and how many times domestication occurred. We provided a brief summary of bioactive compounds naturally occurring in these species that are fundamental for human wellbeing. The great number of wild lineages is a key point to improve landraces since the domestication process caused a loss of gene diversity. Their genomes hide a precious gene pool yet mostly unexplored, and genes lost during human activity can be recovered from the wild lineages and reintroduced in cultivated forms through modern technologies. Finally, we describe how all this information is game-changing to the design of future crops by domesticating de novo.

With no lysine kinases: the key regulatory networks and phytohormone cross talk in plant growth, development and stress response

With No Lysine kinases (WNKs) are a distinct family of Serine/Threonine protein kinase with unique arrangement of catalytic residues in kinase domain. In WNK, an essential catalytic lysine requisite for attaching ATP and phosphorylation reaction is located in subdomain I, instead of subdomain II, which is essentially a typical feature of other Ser/Thr kinases. WNKs are identified in diverse organisms including multicellular and unicellular organisms. Mammalian WNKs are well characterized at structural and functional level, while plant WNKs are not explored much except few recent studies. Plant WNKs role in various physiological processes viz. ion maintenance, osmotic stress, pH homeostasis, circadian rhythms, regulation of flowering time, proliferation and organ development, and abiotic stresses are known, but the mechanisms involved are unclear. Plant WNKs are known to be involved in enhanced drought and salt stress response via ABA-signaling pathway, but the complete signaling cascade is yet to be elucidated. The current review will discuss the interplay between WNKs and growth regulators and their cross talks in plant growth and development. We have also highlighted the link between the stress phytohormones and WNK members in regulating abiotic stress responses in plants. The present review will provide an overall known mechanism on the involvement of WNKs in plant growth and development and abiotic stress response and highlight its role/applications in the development of stress-tolerant plants.

Diversity, population structure, and linkage disequilibrium among cowpea accessions

Cowpea [Vigna unguiculata (L.) Walp] is a globally important food security crop. However, it is susceptible to pest and disease; hence, constant breeding efforts based on its diversity are required for its improvement. The present study aims to investigate the genetic diversity, population structure, and linkage disequilibrium (LD) among 274 cowpea accessions from different origins. A total of 3,127 single nucleotide polymorphism (SNP) markers generated using diversity array technology (DArT) was used. Population structure, neighbor-joining clustering, and principal component analyses indicated three subpopulations within the germplasm. Results of STRUCTURE analysis and discriminant analysis of principal components (DAPC) were complementary in assessing the structuration of the diversity among the germplasm, with the grouping of the accessions improved in DAPC. Genetic distances of 0.005-0.44 were observed among accessions. Accessions from western and central Africa, eastern and central Africa, and Asia were predominant and distributed across all subpopulations. The subpopulations had fixation indexes of 0.48-0.56. Analysis of molecular variance revealed that within subpopulation variation accounted for 81% of observed genetic variation in the germplasm. The subpopulations mainly consisted of inbred lines (inbreeding coefficient = 1) with common alleles, although they were from different geographical regions. This reflects considerable seed movement and germplasm exchange between regions. The LD was characterized by low decay for great physical distances between markers. The LD decay distance varied among chromosomes with the average distance of 80-100 kb across the genome. Thus, crop improvement is possible, and the LD will facilitate genome-wide association studies on quality attributes and critical agronomic traits in cowpea.

Introgression Breeding in Cowpea [Vigna unguiculata (L.) Walp.]

The narrow base of genetic diversity characteristic of cowpea can be attributed to it being self-pollinating, evolving from narrow wild germplasm and exhibiting very limited gene flow between wild and cultivated types. Backcrossing to introduce simply inherited desirable traits and utilization of improved breeding lines and varieties as parents in crossing programs further narrowed the genetic base of cowpea varieties. In most cowpea breeding programs, genes for resistance and market traits were pyramided into lines characterized by high levels of acceptance to farmers and consumers. Besides predisposing widely distributed improved varieties to genetic vulnerability, a narrow base of genetic variation may be contributing to the plateauing in cowpea grain yield, which compromises genetic gains. Cross compatible wild relatives have not been used in variety development because breeders shy away from them due to their tiny seed size, unattractive seed coat color and texture, pod shattering, and susceptibility to viruses. A number of wild cowpea relatives, both within and outside section Catiang of Vigna species, have been evaluated for their reaction to cowpea insect pests and diseases. Vigna vexillata lines were resistant to the legume pod borer (Maruca vitrata), the cowpea weevil (Callosobruchus maculatus), and Striga gesnerioides but are cross incompatible with cultivated cowpea. Some lines among the cross compatible wild relative V. unguiculata ssp. dekindtiana were found to be resistant to aphid in the seedling stage, while others showed good levels of drought and heat tolerance. Molecular markers are being generated to identify quantitative trait loci (QTL) with effects on some desirable attributes in cowpea. Modern breeding tools, including transgenics, can be applied for the improvement of cowpea, bypassing the natural barriers of traditional breeding. Transgenic cowpea with Bt gene cry1Ab showing resistance to M. vitrata has been released in Nigeria. Genome editing, a powerful emerging tool, can also be used for developing improved cowpea varieties with durable resistance to pests and diseases.