Gene discovery reveals new biology, expands the utility of marker‐assisted selection, and enables targeted mutagenesis. Still, such discoveries can take over a decade. We present a general strategy, ...“Agile Genetics,” that uses nested, structured populations to overcome common limits on gene resolution. Extensive simulation work on realistic genetic architectures shows that, at population sizes of >5000 samples, single gene‐resolution can be achieved using bulk segregant pools. At this scale, read depth and technical replication become major drivers of resolution. Emerging enrichment methods to address coverage are on the horizon; we describe one possibility – iterative depth sequencing (ID‐seq). In addition, graph‐based pangenomics in experimental populations will continue to maximize accuracy and improve interpretation. Based on this merger of agronomic scale with molecular and bioinformatic innovation, we predict a new age of rapid gene discovery.
Useful variation in crop genes can be precisely identified using Agile Genetics, a framework for nesting a classical population within a much larger QTL‐seq field study. Pangenomic graphs of founder parents assist each phase of the process, including iterative depth sequencing to maximize resolution at a reduced cost.
Summary
Plant genetic transformation is a crucial step for applying biotechnology such as genome editing to basic and applied plant science research. Its success primarily relies on the efficiency of ...gene delivery into plant cells and the ability to regenerate transgenic plants. In this study, we have examined the effect of several developmental regulators (DRs), including PLETHORA (PLT5), WOUND INDUCED DEDIFFERENTIATION 1 (WIND1), ENHANCED SHOOT REGENERATION (ESR1), WUSHEL (WUS) and a fusion of WUS and BABY‐BOOM (WUS‐P2A‐BBM), on in planta transformation through injection of Agrobacterium tumefaciens in snapdragons (Antirrhinum majus). The results showed that PLT5, WIND1 and WUS promoted in planta transformation of snapdragons. An additional test of these three DRs on tomato (Solanum lycopersicum) further demonstrated that the highest in planta transformation efficiency was observed from PLT5. PLT5 promoted calli formation and regeneration of transformed shoots at the wound positions of aerial stems, and the transgene was stably inherited to the next generation in snapdragons. Additionally, PLT5 significantly improved the shoot regeneration and transformation in two Brassica cabbage varieties (Brassica rapa) and promoted the formation of transgenic calli and somatic embryos in sweet pepper (Capsicum annum) through in vitro tissue culture. Despite some morphological alternations, viable seeds were produced from the transgenic Bok choy and snapdragons. Our results have demonstrated that manipulation of PLT5 could be an effective approach for improving in planta and in vitro transformation efficiency, and such a transformation system could be used to facilitate the application of genome editing or other plant biotechnology application in modern agriculture.
Peanut is one of the most common food triggers of fatal anaphylaxis worldwide although peanut allergy affects only 1%‐2% of the general population. Peanuts are the source of highly potent allergenic ...proteins. It is emerging that the allergenicity of certain proteins is linked to their biological function. Peanut is an unusual crop in that it flowers aboveground but produces its seed‐containing pods underground. This so‐called geocarpic fruiting habit exposes pods and seeds during their development to soilborne pathogens and pests. Pest damage can also open routes of entry for opportunistic fungi such as Aspergillus. Although seed proteins have primary functions in nutrient reservoirs, lipid storage bodies, or the cytoskeleton, they have also evolved to act as part of the plant's defense system to enhance fitness and survival of the species. When interacting with pathogens or pests, these proteins modify and damage cells' membranes, interact with immune receptors, and modulate signaling pathways. Moreover, following exposure, the immune system of predisposed individuals reacts to these proteins with the production of specific IgE. This review explores the evolutionary biology of peanut and its seed proteins and highlights possible links between the proteins' biological function and their allergenicity.
Summary
Multiparental genetic mapping populations such as nested‐association mapping (NAM) have great potential for investigating quantitative traits and associated genomic regions leading to rapid ...discovery of candidate genes and markers. To demonstrate the utility and power of this approach, two NAM populations, NAM_Tifrunner and NAM_Florida‐07, were used for dissecting genetic control of 100‐pod weight (PW) and 100‐seed weight (SW) in peanut. Two high‐density SNP‐based genetic maps were constructed with 3341 loci and 2668 loci for NAM_Tifrunner and NAM_Florida‐07, respectively. The quantitative trait locus (QTL) analysis identified 12 and 8 major effect QTLs for PW and SW, respectively, in NAM_Tifrunner, and 13 and 11 major effect QTLs for PW and SW, respectively, in NAM_Florida‐07. Most of the QTLs associated with PW and SW were mapped on the chromosomes A05, A06, B05 and B06. A genomewide association study (GWAS) analysis identified 19 and 28 highly significant SNP–trait associations (STAs) in NAM_Tifrunner and 11 and 17 STAs in NAM_Florida‐07 for PW and SW, respectively. These significant STAs were co‐localized, suggesting that PW and SW are co‐regulated by several candidate genes identified on chromosomes A05, A06, B05, and B06. This study demonstrates the utility of NAM population for genetic dissection of complex traits and performing high‐resolution trait mapping in peanut.
SUMMARY
Cowpea (Vigna unguiculata (L.) Walp.) is one of the most important legume crops planted worldwide, but despite decades of effort, cowpea transformation is still challenging due to inefficient ...Agrobacterium‐mediated transfer DNA delivery, transgenic selection and in vitro shoot regeneration. Here, we report a highly efficient transformation system using embryonic axis explants isolated from imbibed mature seeds. We found that removal of the shoot apical meristem from the explants stimulated direct multiple shoot organogenesis from the cotyledonary node tissue. The application of a previously reported ternary transformation vector system provided efficient Agrobacterium‐mediated gene delivery, while the utilization of spcN as selectable marker enabled more robust transgenic selection, plant recovery and transgenic plant generation without escapes and chimera formation. Transgenic cowpea plantlets developed exclusively from the cotyledonary nodes at frequencies of 4% to 37% across a wide range of cowpea genotypes. CRISPR/Cas‐mediated gene editing was successfully demonstrated. The transformation principles established here could also be applied to other legumes to increase transformation efficiencies.
Significance Statement
The tissue culture and transformation technology developed herein represents a significant advance in Agrobacterium‐mediated transformation and CRISPR/Cas‐mediated genome editing of an important orphan crop, cowpea (Vigna unguiculata (L.) Walp.). The principles established in this study have the potential to improve the transformation and editing efficiencies not only for cowpea, but also for other legume species, such as soybean (Glycine max) and common bean (Phaseolus vulgaris).
Apomixis, a type of asexual reproduction in angiosperms, results in progenies that are genetically identical to the mother plant. It is a highly desirable trait in agriculture due to its potential to ...preserve heterosis of F
hybrids through subsequent generations. However, no major crops are apomictic. Deciphering mechanisms underlying apomixis becomes one of the alternatives to engineer self-reproducing capability into major crops. Parthenogenesis, a major component of apomixis, commonly described as the ability to initiate embryo formation from the egg cell without fertilization, also can be valuable in plant breeding for doubled haploid production. A deeper understanding of transcriptional differences between parthenogenetic and sexual or non-parthenogenetic eggs can assist with pathway engineering. By conducting laser capture microdissection-based RNA-seq on sexual and parthenogenetic egg cells on the day of anthesis, a de novo transcriptome for the Cenchrus ciliaris egg cells was created, transcriptional profiles that distinguish the parthenogenetic egg from its sexual counterpart were identified, and functional roles for a few transcription factors in promoting natural parthenogenesis were suggested. These transcriptome data expand upon previous gene expression studies and will be a resource for future research on the transcriptome of egg cells in parthenogenetic and sexual genotypes.
The advent of the genome sequences of
and
has ushered in a new era for peanut genomics. With the goal of producing a gene atlas for cultivated peanut (
), 22 different tissue types and ontogenies ...that represent the full development of peanut were sequenced, including a complete reproductive series from flower to peg elongation and peg tip immersion in the soil to fully mature seed. Using a genome-guided assembly pipeline, a homeolog-specific transcriptome assembly for
was assembled and its accuracy was validated. The assembly was used to annotate 21 developmental co-expression networks as tools for gene discovery. Using a set of 8816 putative homeologous gene pairs, homeolog expression bias was documented, and although bias was mostly balanced, there were striking differences in expression bias in a tissue-specific context. Over 9000 alterative splicing events and over 6000 non-coding RNAs were further identified and profiled in a developmental context. Together, this work represents a major new resource for cultivated peanut and will be integrated into peanutbase.org as an available resource for all peanut researchers.
Apomixis is a naturally occurring mode of asexual reproduction in flowering plants that results in seed formation without the involvement of meiosis or fertilization of the egg. Seeds formed on an ...apomictic plant contain offspring genetically identical to the maternal plant. Apomixis has significant potential for preserving hybrid vigor from one generation to the next in highly productive crop plant genotypes. ApomicticPennisetum/Cenchrusspecies, members of the Poaceae (grass) family, reproduce by apospory. Apospory is characterized by apomeiosis, the formation of unreduced embryo sacs derived from nucellar cells of the ovary and, by parthenogenesis, the development of the unreduced egg into an embryo without fertilization. InPennisetum squamulatum (L.) R.Br., apospory segregates as a single dominant locus, the aposporyspecific genomic region (ASGR). In this study, we demonstrate that thePsASGR-BABY BOOM-like(PsASGR-BBML) gene is expressed in egg cells before fertilization and can induce parthenogenesis and the production of haploid offspring in transgenic sexual pearl millet. A reduction ofPsASGR-BBMLexpression in apomictic F₁ RNAi transgenic plants results in fewer visible parthenogenetic embryos and a reduction of embryo cell number compared with controls. Our results endorse a key role forPsASGR-BBMLin parthenogenesis and a newly discovered role for a member of the BBM-like clade of APETALA 2 transcription factors. Induction of parthenogenesis byPsASGR-BBMLwill be valuable for installing parthenogenesis to synthesize apomixis in crops and will have further application for haploid induction to rapidly obtain homozygous lines for breeding.
Key message
Two QTLs on ChrB09 significantly associated with both early and late leaf spots were identified by genome-wide association study in the US peanut mini-core collection.
Early leaf spot ...(ELS) and late leaf spot (LLS) are two serious peanut diseases in the USA, causing tens of millions of dollars of annual economic losses. However, the genetic factors underlying resistance to those diseases in peanuts have not been well-studied. We conducted a genome-wide association study for the two peanut diseases using Affymetrix version 2.0 SNP array with 120 genotypes mainly coming from the US peanut mini-core collection. A total of 46 quantitative trait loci (QTLs) were identified with phenotypic variation explained (PVE) from 10.19 to 24.11%, in which eighteen QTLs are for resistance to ELS and 28 QTLs for LLS. Among the 46 QTLs, there were four and two major QTLs with PVE higher than 16.99% for resistance ELS and LLS, respectively. Of the six major QTLs, five were located on the B sub-genome and only one was on the A sub-genome, which suggested that the B sub-genome has more potential resistance genomic regions than the A sub-genome. In addition, two genomic regions on chromosome B09 were found to provide significant resistance to both ELS and LLS. A total of 74 non-redundant genes were identified as resistance genes, among which, twelve candidate genes were in significant genomic regions including two candidate genes for both ELS and LLS, and other ten candidate genes for ELS. The QTLs and candidate genes obtained from this study will be useful to breed peanuts for resistances to the diseases.
Developing markers linked to key traits has been a focus of peanut (Arachis hypogaea L.) genomics in the postgenome era. Multiple disease resistance traits have been found to be qualitative and ...controlled by major quantitative trait loci (QTL) or even single genes while others are more complex. Southern stem rot (stem rot in short) is a devastating disease of peanut caused by the fungus Sclerotium rolfsii. It has been one of the most damaging diseases of peanut with regard to both cost of control and yield loss in the southeastern United States for the last decade. The disease is initiated annually from sclerotia in the soil. The nonuniform distribution of these propagules leads to the nonuniform development of disease, which makes phenotyping and genetic mapping of resistance difficult. Here we report the mapping of two QTL regions controlling stem rot resistance in peanut. Using careful field evaluation, resistant and susceptible bulks were identified from a recombinant inbred line (RIL) population and subjected to QTL sequencing (QTL‐seq). Developed SNP markers linked to the QTL were validated in a blind selection test by selecting only with markers in a part of the population not used for initial analysis. The lines selected for bulk sequencing also were shown to have strong separation for resistance in an independent field experiment. This work not only delivers markers for marker‐assisted selection (MAS) for an important disease in peanut but shows that QTL‐seq can work effectively even when considering highly complex, and quantitative traits.
PDF
