A Gene for Genetic Background in Zea mays: Fine-Mapping enhancer of teosinte branched1.2 to a YABBY Class Transcription Factor

Multifaceted mechanisms controlling grain disarticulation in the Poaceae

Cereal shattering and threshability, both involving disarticulation of grains from the mother plant, are important traits for cereal domestication and improvement. Recent studies highlighted diverse mechanisms influencing shattering and threshability, either through development of the disarticulation zone or floral structures enclosing or supporting the disarticulation unit. Differential lignification in the disarticulation zone is essential for rice shattering but not required for many other grasses. During shattering, the disarticulation zone undergoes either abscission leading to cell separation or cell breakage. Threshability can be affected by the morphology and toughness of the enclosing floral structures, and in some species, by the inherent weakness of the disarticulation zone. Fine-tuning shattering and threshability is essential for breeding wild and less domesticated cereals.

Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology

The TEOSINTE BRANCHED1 (TBI1), CYCLOIDEA (CYC), and PROLIFERATING CELL NUCLEAR ANTIGEN FACTORS (PCF1 and PCF2) proteins truncated as TCP transcription factors carry conserved basic-helix-loop-helix (bHLH) structure, related to DNA binding functions. Evolutionary history of the TCP genes has shown their presence in early land plants. In this paper, we performed a comparative discussion on the current knowledge of the TCP Transcription Factors in lower and higher plants: their evolutionary history based on the phylogenetics of 849 TCP proteins from 37 plant species, duplication events, and biochemical roles in some of the plants species. Phylogenetics investigations confirmed the classification of TCP TFs into Class I (the PCF1/2), and Class II (the C- clade) factors; the Class II factors were further divided into the CIN- and CYC/TB1- subclade. A trace in the evolution of the TCP Factors revealed an absence of the CYC/TB1subclade in lower plants, and an independent evolution of the CYC/TB1subclade in both eudicot and monocot species. 54% of the total duplication events analyzed were biased towards the dispersed duplication, and we concluded that dispersed duplication events contributed to the expansion of the TCP gene family. Analysis in the TCP factors functional roles confirmed their involvement in various biochemical processes which mainly included promoting cell proliferation in leaves in Class I TCPs, and cell division during plant development in Class II TCP Factors. Apart from growth and development, the TCP Factors were also shown to regulate hormonal and stress response pathways. Although this paper does not exhaust the present knowledge of the TCP Transcription Factors, it provides a base for further exploration of the gene family.

Evolutionary Analysis of the YABBY Gene Family in Brassicaceae

The YABBY gene family is one of the plant transcription factors present in all seed plants. The family members were extensively studied in various plants and shown to play important roles in plant growth and development, such as the polarity establishment in lateral organs, the formation and development of leaves and flowers, and the response to internal plant hormone and external environmental stress signals. In this study, a total of 364 YABBY genes were identified from 37 Brassicaceae genomes, of which 15 were incomplete due to sequence gaps, and nine were imperfect (missing C2C2 zinc-finger or YABBY domain) due to sequence mutations. Phylogenetic analyses resolved these YABBY genes into six compact clades except for a YAB3-like gene identified in Aethionema arabicum. Seventeen Brassicaceae species each contained a complete set of six basic YABBY genes (i.e., 1 FIL, 1 YAB2, 1 YAB3, 1 YAB5, 1 INO and 1 CRC), while 20 others each contained a variable number of YABBY genes (5-25) caused mainly by whole-genome duplication/triplication followed by gene losses, and occasionally by tandem duplications. The fate of duplicate YABBY genes changed considerably according to plant species, as well as to YABBY gene type. These YABBY genes were shown to be syntenically conserved across most of the Brassicaceae species, but their functions might be considerably diverged between species, as well as between paralogous copies, as demonstrated by the promoter and expression analysis of YABBY genes in two Brassica species (B. rapa and B. oleracea). Our study provides valuable insights for understanding the evolutionary story of YABBY genes in Brassicaceae and for further functional characterization of each YABBY gene across the Brassicaceae species.

Natural Variation in Crops: Realized Understanding, Continuing Promise

Crops feed the world's population and shape human civilization. The improvement of crop productivity has been ongoing for almost 10,000 years and has evolved from an experience-based to a knowledge-driven practice over the past three decades. Natural alleles and their reshuffling are long-standing genetic changes that affect how crops respond to various environmental conditions and agricultural practices. Decoding the genetic basis of natural variation is central to understanding crop evolution and, in turn, improving crop breeding. Here, we review current advances in the approaches used to map the causal alleles of natural variation, provide refined insights into the genetics and evolution of natural variation, and outline how this knowledge promises to drive the development of sustainable agriculture under the dome of emerging technologies.

Ectopic Expression of a Pak-choi YABBY Gene, BcYAB3, Causes Leaf Curvature and Flowering Stage Delay in Arabidopsis thaliana

The YABBY family are a group of seed plant-specific transcription factors, which are involved in the specification of abaxial polarity in lateral organs. In Arabidopsis thaliana, YABBY3 (YAB3) plays a critical role in regulating abaxial patterning, growth of lateral organs, and inflorescence phyllotaxy. In this study, the BcYAB3 gene was isolated from Pak-choi (Brassica rapa subsp. chinensis). The tissue-specific expression analysis indicated that the BcYAB3 gene has significantly high transcript levels in stem, leaf, and flower. We investigated the subcellular localization of BcYAB3 and found the protein to be expressed in the nucleus. In the transgenic Arabidopsisthaliana plants expressing the BcYAB3 gene, the leaves were curling downward with the plant growth, and the bolting and flowering stages were delayed. These results not only validate the function of BcYAB3 in the leaf and flower development in Arabidopsis, but also contribute to unravel the molecular regulatory mechanism of YAB3 gene in the establishment of adaxial–abaxial polarity of the lateral organs in Pak-choi.

Molecular characterization of teosinte branched1 gene governing branching architecture in cultivated maize and wild relatives

We sequenced the entire tb1 gene in six maize inbreds and its wild relatives (parviglumis, mexicana, perennis and luxurians) to characterize it at molecular level. Hopscotch and Tourist transposable elements were observed in the upstream of tb1 in all maize inbreds, while they were absent in wild relatives. In maize, tb1 consisted of 431-443 bp 5'UTR, 1101 bp coding sequence and 211-219 bp 3'UTR. In promoter region, mutations in the light response element in mexicana (~ 35 bp and ~ 55 bp upstream of TSS) and perennis (at ~ 35 bp upstream of TSS) were found. A 6 bp insertion at 420 bp downstream of the polyA signal site was present among teosinte accessions, while it was not observed in maize. A codominant marker flanking the 6 bp InDel was developed, and it differentiated the teosintes from maize. In Tb1 protein, alanine (12.7-14.6%) was the most abundant amino acid with tryptophan as the rarest (0.5-0.9%). The molecular weight of Tb1 protein was 38757.15 g/mol except 'Palomero Toluqueno' and HKI1128. R and TCP motifs in Tb1 protein were highly conserved across maize, teosinte and orthologues, while TCP domain differed for tb1 paralogue. Tb1 possessed important role in light-, auxin-, stress-response and meristem identity maintenance. Presence of molecular signal suggested its localization in mitochondria, nucleus and nucleolus. Parviglumis and mexicana shared closer relationship with maize than perennis and luxurians. A highly conserved 59-60 amino acids long bHLH region was observed across genotypes. Information generated here assumes significance in evolution of tb1 gene and breeding for enhancement of prolificacy in maize.

Characterization and T-DNA insertion sites identification of a multiple-branches mutant br in Betula platyphylla × Betula pendula

BACKGROUND

Plant architecture, which is mostly determined by shoot branching, plays an important role in plant growth and development. Thus, it is essential to explore the regulatory molecular mechanism of branching patterns based on the economic and ecological importance. In our previous work, a multiple-branches birch mutant br was identified from 19 CINNAMOYL-COENZYME A REDUCTASE 1 (CCR1)-overexpressed transgenic lines, and the expression patterns of differentially expressed genes in br were analyzed. In this study, we further explored some other characteristics of br, including plant architecture, wood properties, photosynthetic characteristics, and IAA and Zeatin contents. Meanwhile, the T-DNA insertion sites caused by the insertion of exogenous BpCCR1 in br were identified to explain the causes of the mutation phenotypes.

RESULTS

The mutant br exhibited slower growth, more abundant and weaker branches, and lower wood basic density and lignin content than BpCCR1 transgenic line (OE2) and wild type (WT). Compared to WT and OE2, br had high stomatal conductance (Gs), transpiration rate (Tr), but a low non-photochemical quenching coefficient (NPQ) and chlorophyll content. In addition, br displayed an equal IAA and Zeatin content ratio of main branches' apical buds to lateral branches' apical buds and high ratio of Zeatin to IAA content. Two T-DNA insertion sites caused by the insertion of exogenous BpCCR1 in br genome were found. On one site, chromosome 2 (Chr2), no known gene was detected on the flanking sequence. The other site was on Chr5, with an insertion of 388 bp T-DNA sequence, resulting in deletion of 107 bp 5' untranslated region (UTR) and 264 bp coding sequence (CDS) on CORONATINE INSENSITIVE 1 (BpCOII). In comparison with OE2 and WT, BpCOI1 was down-regulated in br, and the sensitivity of br to Methyl Jasmonate (MeJA) was abnormal.

CONCLUSIONS

Plant architecture, wood properties, photosynthetic characteristics, and IAA and Zeatin contents in main and lateral branches' apical buds changed in br over the study's time period. One T-DNA insertion was identified on the first exon of BpCOI1, which resulted in the reduction of BpCOI1 expression and abnormal perception to MeJA in br. These mutation phenotypes might be associated with a partial loss of BpCOI1 in birch.

Overexpression of a soybean YABBY gene, GmFILa, causes leaf curling in Arabidopsis thaliana

BACKGROUND

YABBY genes play important roles in the growth and polar establishment of lateral organs such as leaves and floral organs in angiosperms. However, the functions of YABBY homologous genes are largely unknown in soybean.

RESULTS

In this study, we identified GmFILa encoding a YABBY transcription factor belonging to FIL subfamily. In situ mRNA hybridization analysis indicated that GmFILa had specific expression patterns in leaf as well as in flower bud primordia. Ectopic expression of GmFILa in Arabidopsis thaliana altered the partial abaxialization of the adaxial epidermises of leaves. Besides, GmFILa transgenic plants also exhibited longer flowering period and inhibition of shoot apical meristem (SAM) development compared to the wild type plants. Digital expression data and quantitative real-time polymerase chain reaction (qRT-PCR) analysis demonstrated that the expression of GmFILa was induced by biotic and abiotic stresses and hormone treatments. Transcriptome analysis suggested that overexpressing GmFILa yielded 82 significant differentially expressed genes (DEGs) in Arabidopsis leaves, which can be classified into transcription factors, transporters, and genes involved in growth and development, metabolism, signal transduction, redox reaction and stress response.

CONCLUSIONS

These results not only demonstrate the roles of GmFILa involved in leaf adaxial-abaxial polarity in Arabidopsis, but also help to reveal the molecular regulatory mechanism of GmFILa based on the transcriptomic data.

The genetic architecture of teosinte catalyzed and constrained maize domestication

Crop domestication is a well-established system for understanding evolution. We interrogated the genetic architecture of maize domestication from a quantitative genetics perspective. We analyzed domestication-related traits in a maize landrace and a population of its ancestor, teosinte. We observed strong divergence in the underlying genetic architecture including change in the genetic correlations among traits. Despite striking divergence, selection intensities were low for all traits, indicating that selection under domestication can be weaker than natural selection. Analyses suggest total grain weight per plant was not improved and that genetic correlations placed considerable constraint on selection. We hope our results will motivate crop evolutionists to perform similar work in other crops.

The process of evolution under domestication has been studied using phylogenetics, population genetics–genomics, quantitative trait locus (QTL) mapping, gene expression assays, and archaeology. Here, we apply an evolutionary quantitative genetic approach to understand the constraints imposed by the genetic architecture of trait variation in teosinte, the wild ancestor of maize, and the consequences of domestication on genetic architecture. Using modern teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. We found a reduction in heritabilities across most traits, and the reduction is stronger in reproductive traits (size and numbers of grains and ears) than vegetative traits. We observed larger depletion in additive genetic variance than dominance genetic variance. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. Yield (total grain weight) per plant is the sole trait that selection does not appear to have improved in maize relative to teosinte. From a multivariate evolution perspective, we identified a strong, nonneutral divergence between teosinte and maize landrace genetic variance–covariance matrices (G-matrices). While the structure of G-matrix in teosinte posed considerable genetic constraint on early domestication, the maize landrace G-matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory.

Maize domestication and gene interaction

Contents Summary 395 I. Introduction 395 II. The genetic basis of maize domestication 396 III. The tempo of maize domestication 401 IV. Genetic interactions and selection during maize domestication 401 V. Gene networks of maize domestication alleles 404 VI. Implications of gene interactions on evolution and selection404 VII. Conclusions 405 Acknowledgements 405 References 405 SUMMARY: Domestication is a tractable system for following evolutionary change. Under domestication, wild populations respond to shifting selective pressures, resulting in adaptation to the new ecological niche of cultivation. Owing to the important role of domesticated crops in human nutrition and agriculture, the ancestry and selection pressures transforming a wild plant into a domesticate have been extensively studied. In Zea mays, morphological, genetic and genomic studies have elucidated how a wild plant, the teosinte Z. mays subsp. parviglumis, was transformed into the domesticate Z. mays subsp. mays. Five major morphological differences distinguish these two subspecies, and careful genetic dissection has pinpointed the molecular changes responsible for several of these traits. But maize domestication was a consequence of more than just five genes, and regions throughout the genome contribute. The impacts of these additional regions are contingent on genetic background, both the interactions between alleles of a single gene and among alleles of the multiple genes that modulate phenotypes. Key genetic interactions include dominance relationships, epistatic interactions and pleiotropic constraint, including how these variants are connected in gene networks. Here, we review the role of gene interactions in generating the dramatic phenotypic evolution seen in the transition from teosinte to maize.

Selection During Maize Domestication Targeted a Gene Network Controlling Plant and Inflorescence Architecture

Selection during evolution, whether natural or artificial, acts through the phenotype. For multifaceted phenotypes such as plant and inflorescence architecture, the underlying genetic architecture is comprised of a complex network of interacting genes rather than single genes that act independently to determine the trait. As such, selection acts on entire gene networks. Here, we begin to define the genetic regulatory network to which the maize domestication gene, teosinte branched1 (tb1), belongs. Using a combination of molecular methods to uncover either direct or indirect regulatory interactions, we identified a set of genes that lie downstream of tb1 in a gene network regulating both plant and inflorescence architecture. Additional genes, known from the literature, also act in this network. We observed that tb1 regulates both core cell cycle genes and another maize domestication gene, teosinte glume architecture1 (tga1). We show that several members of the MADS-box gene family are either directly or indirectly regulated by tb1 and/or tga1, and that tb1 sits atop a cascade of transcriptional regulators controlling both plant and inflorescence architecture. Multiple members of the tb1 network appear to have been the targets of selection during maize domestication. Knowledge of the regulatory hierarchies controlling traits is central to understanding how new morphologies evolve.