Collection
Plant Genetics and Genomics
Plant science has generated many discoveries and advances in genetics and genomics research. These contributions reflect the ingenuity and rigor of the plant science community, as well as the rich diversity of plants and their biology. Plants are vital in our daily lives—as a source of food, fiber, and fuel—and as a key component of the global carbon cycle. As such, the importance of plant research should not be underestimated, especially as society copes with changing climate and its impacts to crop productivity and sustainable energy.
To showcase this critical work, GENETICS and G3: Genes|Genomes|Genetics launched the Plant Genetics and Genomics series in February 2023 with a collection of fourteen research articles and an accompanying editorial. This launch block of papers was overseen by editors Thomas E. Juenger (University of Texas at Austin), Andrea L. Sweigart (University of Georgia), Jianming Yu (Iowa State University), and James Birchler (University of Missouri at Columbia). Authors are invited to submit manuscripts to the series on an ongoing basis.
Flower color plays a crucial role in the appeal and selection of ornamental plants, directly influencing breeding strategies and the broader horticulture industry. Lantana camara , a widely favored flowering shrub, presents a rich palette of flower colors. Yet, the intricate molecular mechanisms ...
Hop production utilizes exclusively female plants, whereas male plants only serve to generate novel variation within breeding programs through crossing. Currently, hop lacks a rapid and accurate diagnostic marker to determine whether plants are male or female. Without a diagnostic marker, breeding ...
The US standard for maize commercially grown for grain specifies that yellow corn can contain at maximum 5% corn of other colors. Inbred parents of commercial hybrids typically have clear pericarp, but transgressive segregants in breeding populations can display variation in pericarp pigmentation. ...
The balanced segregation of homologous chromosomes during meiosis is essential for fertility and is mediated by crossovers (COs). A strong reduction of CO number leads to the unpairing of homologous chromosomes after the withdrawal of the synaptonemal complex. This results in the random segregation ...
Apple scab, a fungal disease caused by Venturia inaequalis , leads to losses in both yield and fruit quality of apples ( Malus domestica Borkh.). Most commercial apple cultivars, including those containing the well-characterized Rvi6- scab-resistance locus on linkage group (LG) 1, are susceptible ...
Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, ...
Speciation of cultivated peanut has greatly reduced its genetic diversity, leading to challenges with crop yield. The Groundnut Improvement Network in Africa (GINA) assemble a collection of 1049 peanut breeding lines, varieties, and landraces from nine African countries and use a high-density SNP array to analyze the genetic structure of the collection and quantify levels of genetic diversity. The authors develop a core collection of 300 lines based on breeding traits and genetic diversity, sharing it as a resource for breeding and discovery purposes.
The highly active family of Mutator ( Mu ) DNA transposons has been widely used for forward and reverse genetics in maize. There are examples of Mu -suppressible alleles that result in conditional phenotypic effects based on the activity of Mu . Phenotypes from these Mu -suppressible mutations are ...
Rice hoja blanca (RHB) is one of the most serious diseases in rice-growing areas in tropical Americas. Its causal agent is RHB virus (RHBV), transmitted by the planthopper Tagosodes orizicolus Müir. Genetic resistance is the most effective and environment-friendly way of controlling the disease. So ...
A population encounters a variety of environmental stresses, so the full source of its resilience can only be captured by collecting all the signatures of adaptation to the selection of the local environment in its population history. Based on the multiomic data of Arabidopsis thaliana , we ...
Lettuce ( Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. To breed resilient and resistant lettuce in the future, valuable genetic variation found in close relatives could be further exploited. Lactuca ...
Northern red oak ( Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first ...
Promoters regulate both the amplitude and pattern of gene expression—key factors needed for optimization of many synthetic biology applications. Previous work in Arabidopsis found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular ...
The Ga1 locus controls cross-incompatibility between field corn and popcorn. The Ga1 - S haplotype contains 2 types of pectin methylesterase (PME) genes, ZmPme3 and several copies of ZmGa1P that are expressed in silk and pollen, respectively. The ga1 haplotype contains nonfunctional tandem repeat ...
Using whole genome and transcriptomic sequencing of extremely resistant and susceptible maize lines to the Gram-positive bacterial disease, Goss’s wilt, along with traditional genome-wide association mapping, quantitative trait locus analysis, and comparison of near-isogenic lines, Hao et al. identified association loci and the genes commonly and differentially responding to the bacterium in resistant and susceptible maize lines. Integration of omics’ data led to the findings of multiple well-evidenced candidate genes that are responsible for host resistance.
To improve resolution to small genomic regions and sensitivity to small-effect loci in the identification of genetic factors conferring the enlarged inflorescence and other traits of cauliflower while also expediting further genetic dissection, 104 near-isogenic introgression lines (NIILs) covering ...
Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress–tolerant varieties and genes that could limit future climate-changed–induced yield ...
The evolution of genomic incompatibilities causing postzygotic barriers to hybridization is a key step in species divergence. Incompatibilities take 2 general forms—structural divergence between chromosomes leading to severe hybrid sterility in F 1 hybrids and epistatic interactions between genes ...
In plastids, conversion of light energy into ATP relies on cytochrome f , a key electron carrier with a heme covalently attached to a CXXCH motif. Covalent heme attachment requires reduction of the disulfide-bonded CXXCH by CCS5 and CCS4. CCS5 receives electrons from the oxidoreductase CCDA, while ...
DNA methylation in plants is depleted from cis-regulatory elements in and near genes but is present in some gene bodies, including exons. Methylation in exons solely in the CG context is called gene body methylation (gbM). Methylation in exons in both CG and non-CG contexts is called TE-like ...
The juvenilized phenotype of Teopod1 (Tp1) and Teopod2 (Tp2) mutations provided the first evidence that vegetative phase change in plants is genetically regulated. This paper demonstrates that Tp1 and Tp2 are hypermorhphic mutations in, respectively, Zma-miR156j and Zma-miR156h, that lead to the over-expression of miR156. Recessive alleles of Early Phase Change (epc) have the opposite phenotype, and represent mutations in the maize orthologue of HASTY, a gene required for the stability of miRNAs.
African rice ( Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice ( Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better ...
In maize, the community-standard transformant line B104 is a useful model for dissecting features of transfer DNA (T-DNA) integration due to its compatibility with Agrobacterium -mediated transformation and the availability of its genome sequence. Knowledge of transgene integration sites permits ...
Advances in DNA sequencing technologies allow the sequencing of whole genomes of thousands of individuals and provide several million single nucleotide polymorphisms (SNPs) per individual. These data combined with precise and high-throughput phenotyping enable genome-wide association studies (GWAS) ...
Ecological isolation is increasingly thought to play an important role in speciation, especially for the origin and reproductive isolation of homoploid hybrid species. However, the extent to which divergent and/or transgressive gene expression changes are involved in speciation is not well studied. ...
Wine cultivars are available to growers in multiple clonal selections with agronomic and enological differences. Phenotypic differences between clones originated from somatic mutations that accrued over thousands of asexual propagation cycles. Genetic diversity between grape cultivars remains ...
The gene balance hypothesis proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions of networks, pathways, and protein complexes to maintain balanced stoichiometry of interacting proteins, because perturbations to stoichiometric balance can result in ...
Bidirectional flow of information shapes the outcome of the host–pathogen interactions and depends on the genetics of each organism. Recent work has begun to use co-transcriptomic studies to shed light on this bidirectional flow, but it is unclear how plastic the co-transcriptome is in response to ...
WUSCHEL ( WUS ) and WUSCHEL - RELATED HOMEOBOX ( WOX ) encode transcription factors and play important roles in regulating the formation and maintenance of shoot and floral meristems. OsWUS have distinct functions in meristem development with slightly tuned expression. However, the mechanisms ...
De novo transcriptome assembly of next-generation sequencing information has become a powerful tool for the study of non-model species. Transcriptomes generated by this method can have high variability due to endless combinations of user-defined variables and programs available for assembly. Many ...
Elucidating genotype-by-environment interactions is fundamental for understanding the interplay between genetic and environmental factors that shape complex traits in crops. Genotype-by-environment interactions are of practical importance, as they determine the performance of cultivars grown in ...
Switchgrass can be used as an alternative source for bioenergy production. Many breeding programs focus on the genetic improvement of switchgrass for increasing biomass yield. Quantitative trait loci (QTL) mapping can help to discover marker-trait associations and accelerate the breeding process ...
Adaptive genetic diversity in crop wild relatives (CWRs) can be exploited to develop improved crops with higher yield and resilience if phylogenetic relationships between crops and their CWRs are resolved. This further allows accurate quantification of genome-wide introgression and determination of ...
By hybridization and special sexual reproduction, we sequentially aggregated Zea mays , Zea perennis , and Tripsacum dactyloides in an allohexaploid, backcrossed it with maize, derived self-fertile allotetraploids of maize and Z. perennis by natural genome extraction, extended their first six ...
Understanding the genetic basis responding to nitrogen (N) fertilization in crop production is a long-standing research topic in plant breeding and genetics. Albeit years of continuous efforts, the genetic architecture parameters, such as heritability, polygenicity, and mode of selection, ...
Tomáš Brůna, Rishi Aryal, Olga Dudchenko, Daniel James Sargent, Daniel Mead, Matteo Buti, et al.
G3 Genes|Genomes|Genetics, jkac289, https://doi.org/10.1093/g3journal/jkac289
Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus...
Tzitziki Lemus, Grace Alex Mason, Kerry L Bubb, Cristina M Alexandre, Christine Queitsch, Josh T Cuperus
Genetics, iyac163, https://doi.org/10.1093/genetics/iyac163
Argonaute 1 (AGO1), the principal protein component of microRNA-mediated regulation, plays a key role in plant growth and development. AGO1 physically interacts with the chaperone HSP90, which buffers cryptic genetic variation in plants and animals. We sought to determine whether genetic perturbation of AGO1 in Arabidopsis thaliana...
Craig H Carlson, Jason D Fiedler, Sepehr Mohajeri Naraghi, Eric S Nazareno, Naa Korkoi Ardayfio, Michael S McMullen, Shahryar F Kianian
Genetics, iyac128, https://doi.org/10.1093/genetics/iyac128
There is limited information regarding the morphometric relationships of panicle traits in oat (Avena sativa) and their contribution to phenology and growth, physiology, and pathology traits important for yield. To model panicle growth and development and identify genomic regions associated with corresponding traits...
Weier Guo, Luca Comai, Isabelle M Henry
G3 Genes|Genomes|Genetics, jkac185, https://doi.org/10.1093/g3journal/jkac185
Chromoanagenesis is a catastrophic event that involves localized chromosomal shattering and reorganization. In this study, we report a case of chromoanagenesis resulting from defective meiosis in the MEIOTIC ASYNAPTIC MUTANT 1 (asy1) background in Arabidopsis thaliana. We provide a detailed characterization of the genomic structure...
Sharu Paul Sharma, Thomas Peterson
Genetics, iyac124, https://doi.org/10.1093/genetics/iyac124
Eukaryotic genomes are large and complex, and gene expression can be affected by multiple regulatory elements and their positions within the dynamic chromatin architecture. Transposable elements are known to play important roles in genome evolution, yet questions remain as to how transposable elements alter genome structure and affect gene expression...
Atsumi Ando, Ryan C Kirkbride, Hong Qiao, Z Jeffrey Chen
Genetics, iyac161, https://doi.org/10.1093/genetics/iyac161
Seed size is related to plant evolution and crop yield and is affected by genetic mutations, imprinting, and genome dosage. Imprinting is a widespread epigenetic phenomenon in mammals and flowering plants. ETHYLENE INSENSITIVE2 (EIN2) encodes a membrane protein that links the ethylene perception to transcriptional regulation...
Jyoti Saini Sharma, Curt A McCartney, Brent D McCallum, Colin W Hiebert
G3 Genes|Genomes|Genetics, jkac274, https://doi.org/10.1093/g3journal/jkac274
Wheat leaf rust is caused by the fungal pathogen Puccinia triticina and is one of the wheat diseases of concern globally. Among the known leaf rust resistance genes (Lr) genes, Lr32 is a broadly effective gene derived from the diploid species Aegilops tauschii coss. accession RL5497-1 and has been genetically mapped to chromosome arm 3DS. However, Lr32 resistance has not been utilized...
William Palmer, Ewelina Jacygrad, Sagayamary Sagayaradj, Keri Cavanaugh, Rongkui Han, et al.
G3 Genes|Genomes|Genetics, jkac317, https://doi.org/10.1093/g3journal/jkac317
Understanding the basis of hybrid vigor remains a key question in crop breeding and improvement, especially for rootstock development where F1 hybrids are extensively utilized. Full-sibling UCB-1 F1 seedling rootstocks are widely planted in commercial pistachio orchards that are generated by crossing 2 highly heterozygous outbreeding parental...
Gbemisola Okunlola, Baffour Badu-Apraku, Omolayo Ariyo, Paterne Agre, Queen Offernedo, Moninuola Ayo-Vaughan
G3 Genes|Genomes|Genetics, jkac237, https://doi.org/10.1093/g3journal/jkac237
Identification of genes associated with Striga resistance is invaluable for accelerating genetic gains in breeding for Striga resistance in maize. We conducted a genome-wide association study to identify genomic regions associated with grain yield and other agronomic traits under artificial Striga field infestation...
Yousef Rahimi, Bahman Khahani, Ali Jamali, Hadi Alipour, Mohammad Reza Bihamta, Pär K Ingvarsson
G3 Genes|Genomes|Genetics, jkac320, https://doi.org/10.1093/g3journal/jkac320
A genome-wide association study (GWAS) was used to identify associated loci with early vigor under simulated water deficit and grain yield under field drought in a diverse collection of Iranian bread wheat landraces. In addition, a meta-quantitative trait loci (MQTL) analysis was used to further expand our approach by retrieving already published quantitative trait loci (QTL) from recombinant...
Patrick Woods, Nicholas Price, Paul Matthews, John K McKay
G3 Genes|Genomes|Genetics, jkac209, https://doi.org/10.1093/g3journal/jkac209
A comprehensive understanding of the degree to which genomic variation is maintained by selection vs. drift and gene flow is lacking in many important species such as Cannabis sativa, one of the oldest known crops to be cultivated by humans worldwide. We generated whole genome resequencing data across diverse samples of feralized and domesticated lineages of C...
Amanda R Peters Haugrud, Qijun Zhang, Andrew J Green, Steven S Xu, Justin D Faris
G3 Genes|Genomes|Genetics, jkac281, https://doi.org/10.1093/g3journal/jkac281
Crop yield gains are needed to keep pace with a growing global population and decreasing resources to produce food. Cultivated emmer wheat is a progenitor of durum wheat and a useful source of genetic variation for trait improvement in durum. Here, we evaluated a recombinant inbred line population derived from a cross between the North Dakota durum wheat variety Divide...
Edwin Solares, Abraham Morales-Cruz, Rosa Figueroa Balderas, Eric Focht, Vanessa E T M Ashworth, et al.
G3 Genes|Genomes|Genetics, jkac323, https://doi.org/10.1093/g3journal/jkac323
The domestication history of the avocado (Persea americana) remains unclear. We created a reference genome from the Gwen varietal, which is closely related to the economically dominant Hass varietal. Our genome assembly had an N50 of 3.37 megabases, a BUSCO score of 91%, and was scaffolded with a genetic map, producing 12 pseudo-chromosomes with 49,450 genes...
Zhi-Wei Liu, Xing-Yun Shi, Shuang-Mei Duan, Bo Nian, Li-Jiao Chen, Guang-Hui Zhang, Cai-You Lv, Yan Ma, Ming Zhao
G3 Genes|Genomes|Genetics, jkac297, https://doi.org/10.1093/g3journal/jkac297
Flavonoids are rich in tea plants (Camellia sinensis), and responsible for the flavor and healthful benefits of tea beverage. The anthocyanin levels in the purple tender shoots are higher than in the general green leaves of tea plant, which provide special materials to search metabolic mechanisms of flavonoid enrichment in plant...
Virginia T Scarlett, John T Lovell, Mingqin Shao, Jeremy Phillips, Shengqiang Shu, Joanna Lusinska, David M Goodstein, et al.
Genetics, iyac146, https://doi.org/10.1093/genetics/iyac146
The “genomic shock” hypothesis posits that unusual challenges to genome integrity such as whole genome duplication may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and derepression of transposable elements in the immediate aftermath...
Vidya Oruganti, Helena Toegelová, Aleš Pečinka, Andreas Madlung, Korbinian Schneeberger
Genetics, iyac132, https://doi.org/10.1093/genetics/iyac132
Gene flow between species in the genus Arabidopsis occurs in significant amounts, but how exactly gene flow is achieved is not well understood. Polyploidization may be one avenue to explain gene flow between species. One problem, however, with polyploidization as a satisfying explanation is the occurrence of lethal genomic...
Michael Busche, Sarah Hake, Jacob O Brunkard
Genetics, iyac182, https://doi.org/10.1093/genetics/iyac182
Higher plants generate new leaves from shoot meristems throughout their vegetative lifespan. The tempo of leaf initiation is dynamically regulated by physiological cues, but little is known about the underlying genetic signaling pathways that coordinate this rate. Two maize (Zea mays) mutants, terminal ear1 (te1) and phytochrome...
Tayyaba Andleeb, Emilie Knight, Philippa Borrill
G3 Genes|Genomes|Genetics, jkac275, https://doi.org/10.1093/g3journal/jkac275
Senescence enables the remobilization of nitrogen and micronutrients from vegetative tissues of wheat (Triticum aestivum L.) into the grain. Understanding the molecular players in this process will enable the breeding of wheat lines with tailored grain nutrient content. The NAC transcription factor NAM-B1 is associated...
