Amid a rapidly growing global population and increasing threats to crop yields, this review focuses on Speed Breeding (SB) in crop genetics. It traces SB’s development from carbon arc lamp experiments 150 years ago to its modern use with LED technology which significantly accelerates breeding cycles. SB has applications in genetic mapping, genetic modification, and trait stacking, enhancing crop resilience by leveraging allelic diversity. It aligns well with breeding methods like single plant selection and single seed descent. The integration of SB with gene editing, genotyping, and genomic selection holds great promise. However, SB faces challenges related to infrastructure, genotypic variations, and potential stress responses. In summary, SB is a powerful and promising approach to address food security concerns and advancing crop genetics.

Cowpea is one of the most popular dry-land legumes cultivated for food and forage in arid and semi-arid areas. Genetic diversity for global germplasm can be organized into core collections providing optimum resources to serve breeding requirements. Here, we present diversity analysis and genome-wide association study (GWAS) results for part of the cowpea core collection of the United States Department of Agriculture (USDA) along with breeding line controls. Included in the analysis were a total of 373 accessions analyzed with 6880 Single Nucleotide Polymorphism (SNP) markers from Genotyping by Sequencing (GBS). Population structure differentiated accessions into two groups irrespective of geographical origin and formed three clusters based on taxa upon phylogenetic analysis. A total of 56 SNPs were significantly associated to nine traits including pod length (25 Quantitative Trait Nucleotides, QTNs), seed anti-oxidant content (7 QTNs), dry pod color (7 QTNs), plant maturity (5 QTNs), flower color (5 QTNs), seed weight (4 QTNs), tolerance to low phosphate (1 QTN), growth habit (1 QTN), and response to rock phosphate (1 QTN) using Bayesian-information, Linkage-disequilibrium Iteratively Nested Keyway (BLINK), and Fixed and random model Circulating Probability Unification (FarmCPU) association models. Key genes related to all significant SNPs were identified based on annotations of the cowpea reference genome, including a flavonoid gene controlling flower color (Vigun08g040200.1), a root nodulation regulator for tolerance to low phosphate (Vigun11g168000.1), and numerous genes involved in signaling, biosynthesis, metabolite transport, and abiotic stress. Our results highlight the importance of maintaining public phenotyping databases at USDA and strengthening collaborations for data collection in cowpea to maximize research impacts.

The Hydrangea genus belongs to the Hydrangeaceae family, in the Cornales order of flowering plants, which early diverged among the Asterids, and includes several species that are commonly used ornamental plants. Of them, Hydrangea macrophylla is one of the most valuable species in the nursery trade, yet few genomic resources are available for this crop or closely related Asterid species. Two high-quality haplotype-resolved reference genomes of hydrangea cultivars ‘Veitchii’ and ‘Endless Summer’ [highest quality at 2.22 gigabase pairs (Gb), 396 contigs, N50 22.8 megabase pairs (Mb)] were assembled and scaffolded into the expected 18 pseudochromosomes. Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants, nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids. Genetic mapping with an F₁ hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape, CYP78A5 located on chromosome 4, and a novel gene, BAM3 located on chromosome 17, for causing double flower. Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants, the Asterids.

Background: Vanillin is the most abundant volatile compound in natural vanilla extract and the primary metabolite from an economic perspective. Natural vanilla is the second most expensive spice in the world and the most profitable crop adapted to the warm tropics. Despite its global popularity, vanilla is mainly cultivated from vegetatively propagated clones and insufficient modern plant breeding has been achieved. One of the breeding objectives is to increase the vanillin concentration in the cured vanilla capsules. The vanillin biosynthesis pathway has not been thoroughly deciphered and multiple hypotheses are considered. Results: A comparative transcriptomic approach between two accessions with contrasting vanillin content was used to fill in knowledge gaps on vanillin biosynthesis and identify potential candidate genes affecting vanillin accumulation. Out of the 59,128 genes known in vanilla, putative positive and negative regulators that influence vanillin accumulation through pathway modulation, precursor sequestration or enzymatic efficiency were identified. Differentially expressed genes were identified using three specific comparisons on accession, tissue type and developmental stage of capsule. Each comparison was analyzed separately focusing specifically on the accession contrast. BLAST annotation of differentially expressed genes provided protein identities that were mapped to the prominent vanillin biosynthetic pathways proposed by previous studies. Conclusion: Enzymes from the lignin biosynthetic pathway were found to be negatively correlated to vanillin accumulation in vanilla cured capsules. There were 656 differentially expressed genes shared among all three comparisons and included β-glucosidase, cytochrome P450 and PAL amongst others. These results identify gene targets that could lead to higher vanillin content in vanilla cured capsules.

Vanilla orchids are members of the Vanilloideae orchid subfamily, and they hold significant economic value as a spice crop in tropical regions. Despite the presence of 180 known species within this subfamily, commercial production focuses on only three species (Vanilla planifolia, V. odorata, and V. pompona) and one hybrid (V. × tahitensis), prized for their aromatic qualities and bioactive compounds. Limited modern breeding initiatives have been undertaken with vanilla orchids, although recent advancements in genomic research are shedding light on this crop’s potential. The protracted breeding cycle of vanilla, coupled with increasing demand for germplasm, underscores the importance of research and breeding efforts in vanilla. This paper outlines a protocol for haploid production in V. planifolia using unfertilized ovaries in tissue culture conditions. Additionally, we present a methodology to confirm the haploid nature of putative haploid lines through stomatal size comparison, chromosome counting, and flow cytometry analysis, proving the successful development of haploid vanilla plants. These findings contribute to the advancement of breeding programs and genetic improvement strategies for the vanilla industry.

Endophytic bacteria from pea (Pisum sativum L.) plants play important roles in regulating plant growth, health, and nutrition. To enhance the understanding of endophytic bacteria in peas, twenty pea cultivars, two chickpeas, and two broad bean cultivars were planted into artificial soils for 4 weeks. Leaves and roots were collected from plants and sterilized. Endophytic bacterial DNAs were isolated from sterilized materials (leaves, roots, and seeds) and used as templates to detect the bacterial diversity by amplifying the 16S V3–V4 region. The Remel Tryptose Soya Agar (TSA) medium, the aluminum sec-butoxide (ASb) medium, and the yeast extract mannitol agar (YMA) medium were used to isolate bacteria from sterilized leaves and roots, respectively. The plant growth-promoting (PGP) properties of these isolated bacteria, such as the solubilization of phosphorus and potassium and the production of Indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, nitrogenase, pectinase, and cellulose, were studied in vitro. Bacterial isolates were processed for 16S rDNA gene sequencing and performed molecular identification by reconstruction of the phylogenetic tree using the neighborhood association approach in the software MEGA X. Results indicated that the majority of the bacterial communities were shared among leaves, roots, and seeds of pea plants. In both the leaves and roots of pea plants, the prominent phyla identified were Pseudomonadota, Bacteroidota, and Bacillota, with dominant genera such as Rhizobium, Bacteroides, Blautia, and Prevotella prevailing at the genus level. The samples from leaves and roots had unique dominant bacterial genera. In total, 48 endophytic bacteria strains were isolated from leaves and roots, of which 16 strains were from roots and 32 strains were from leaves. The majority of the isolates from leaves (78.13%) and roots (75%) had the ability to produce indole-3-acetic acid (IAA). Moreover, isolates from roots also had greater ability to produce 1-amino-cyclopropane-1-carboxylic acid (ACC) deaminase (81.25%) than those from leaves (62.5%). This study demonstrated the unique distribution of endophytes in leaves and roots of pea, which can have great potential in pea production.