The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning

Multi-Locus Genome-Wide Association Studies for 14 Main Agronomic Traits in Barley

The agronomic traits, including morphological and yield component traits, are important in barley breeding programs. In order to reveal the genetic foundation of agronomic traits of interest, in this study 122 doubled haploid lines from a cross between cultivars "Huaai 11" (six-rowed and dwarf) and "Huadamai 6" (two-rowed) were genotyped by 9680 SNPs and phenotyped 14 agronomic traits in 3 years, and the two datasets were used to conduct multi-locus genome-wide association studies. As a result, 913 quantitative trait nucleotides (QTNs) were identified by five multi-locus GWAS methods to be associated with the above 14 traits and their best linear unbiased predictions. Among these QTNs and their adjacent genes, 39 QTNs (or QTN clusters) were repeatedly detected in various environments and methods, and 10 candidate genes were identified from gene annotation. Nineteen QTNs and two genes (sdw1/denso and Vrs1) were previously reported, and eight candidate genes need to be further validated. The Vrs1 gene, controlling the number of rows in the spike, was found to be associated with spikelet number of main spike, spikelet number per plant, grain number per plant, grain number per spike, and 1,000 grain weight in multiple environments and by multi-locus GWAS methods. Therefore, the above results evidenced the feasibility and reliability of genome-wide association studies in doubled haploid population, and the QTNs and their candidate genes detected in this study are useful for marker-assisted selection breeding, gene cloning, and functional identification in barley.

The Tomato BLADE ON PETIOLE and TERMINATING FLOWER Regulate Leaf Axil Patterning Along the Proximal-Distal Axes

Leaf axil patterning occurs concomitantly with leaf development and takes place at the boundary zone which demarcates the initiating leaf primordium from the shoot apical meristem. Subsequent growth and differentiation result in establishment of the axillary meristem and abscission zone (AZ) along the proximal-distal axis of the leaf axil, yet the molecular mechanisms that regulate these events are poorly understood. We studied the role of the tomato BLADE ON PETIOLE (SlBOP) boundary gene family on the development of the leaf axil using BOP-silenced plants as well as BOP-mutated lines. We show that silencing of the tomato SlBOP gene family affects patterning of the leaf axil along the proximal-distal axis, manifested by dispositioning of the AM and abnormal development of the adjacent tissue resulting in lack of a functional leaf AZ. Dissection of the role of each of the three tomato SlBOPs by analysis of single, double and triple null-mutants demonstrated that SlBOP2 is the dominant gene in leaf axil patterning, but does not rule out involvement of SlBOP1 and SlBOP3 in correct AM positioning. We further studied the potential role of TERMINATING FLOWER (TMF), a transcription factor which was previously shown to interact with SlBOPs, in leaf axil patterning using TMF mutant tomato lines. The results suggest that similar to SlBOP2, TMF is involved in leaf axil proximal-distal patterning and AZ development.

Ideal crop plant architecture is mediated by tassels replace upper ears1, a BTB/POZ ankyrin repeat gene directly targeted by TEOSINTE BRANCHED1

Axillary branch suppression is a favorable trait bred into many domesticated crop plants including maize compared with its highly branched wild ancestor teosinte. Branch suppression in maize was achieved through selection of a gain of function allele of the teosinte branched1 (tb1) transcription factor that acts as a repressor of axillary bud growth. Previous work indicated that other loci may function epistatically with tb1 and may be responsible for some of its phenotypic effects. Here, we show that tb1 mediates axillary branch suppression through direct activation of the tassels replace upper ears1 (tru1) gene that encodes an ankyrin repeat domain protein containing a BTB/POZ motif necessary for protein-protein interactions. The expression of TRU1 and TB1 overlap in axillary buds, and TB1 binds to two locations in the tru1 gene as shown by chromatin immunoprecipitation and gel shifts. In addition, nucleotide diversity surveys indicate that tru1, like tb1, was a target of selection. In modern maize, TRU1 is highly expressed in the leaf trace vasculature of axillary internodes, while in teosinte, this expression is highly reduced or absent. This increase in TRU1 expression levels in modern maize is supported by comparisons of relative protein levels with teosinte as well as by quantitative measurements of mRNA levels. Hence, a major innovation in creating ideal maize plant architecture originated from ectopic overexpression of tru1 in axillary branches, a critical step in mediating the effects of domestication by tb1.

Enhancing crop yield by optimizing plant developmental features

A number of plant features and traits, such as overall plant architecture, leaf structure and morphological features, vascular architecture and flowering time are important determinants of photosynthetic efficiency and hence the overall performance of crop plants. The optimization of such developmental traits thus has great potential to increase biomass and crop yield. Here, we provide a comprehensive review of these developmental traits in crop plants, summarizing their genetic regulation and highlighting the potential of manipulating these traits for crop improvement. We also briefly review the effects of domestication on the developmental features of crop plants. Finally, we discuss the potential of functional genomics-based approaches to optimize plant developmental traits to increase yield.

DORNRÖSCHEN, DORNRÖSCHEN-LIKE, and PUCHI redundantly control floral meristem identity and organ initiation in Arabidopsis

The biphasic floral transition in Arabidopsis thaliana involves many redundant intersecting regulatory networks. The related AP2 transcription factors DORNRÖSCHEN (DRN), DORNRÖSCHEN-LIKE (DRNL), and PUCHI individually execute well-characterized functions in diverse developmental contexts, including floral development. Here, we show that their combined loss of function leads to synergistic floral phenotypes, including reduced floral merosity in all whorls, which reflects redundant functions of all three genes in organ initiation rather than outgrowth. Additional loss of BLADE-ON-PETIOLE1 (BOP1) and BOP2 functions results in the complete conversion of floral meristems into secondary inflorescence shoots, demonstrating that all five genes define an essential regulatory network for establishing floral meristem identity, and we show that their functions converge to regulate LEAFY expression. Thus, despite their largely discrete spatiotemporal expression domains in the inflorescence meristem and early floral meristem, PUCHI, DRN, and DRNL interdependently contribute to cellular fate decisions. Auxin might represent one potential non-cell-autonomous mediator of their gene functions, because PUCHI, DRN, and DRNL all interact with auxin transport and biosynthesis pathways.

Control of inflorescence architecture in tomato by BTB/POZ transcriptional regulators

In tomatoes, formation of multiflowered inflorescences depends on a precisely timed process of meristem maturation mediated by the transcription factor gene TERMINATING FLOWER (TMF). Xu et al. show that TMF protein acts together with homologs of the Arabidopsis BLADE-ON-PETIOLE (BOP) transcriptional cofactors, defined by the conserved BTB/POZ domain.

Plant productivity depends on inflorescences, flower-bearing shoots that originate from the stem cell populations of shoot meristems. Inflorescence architecture determines flower production, which can vary dramatically both between and within species. In tomato plants, formation of multiflowered inflorescences depends on a precisely timed process of meristem maturation mediated by the transcription factor gene TERMINATING FLOWER (TMF), but the underlying mechanism is unknown. We show that TMF protein acts together with homologs of the Arabidopsis BLADE-ON-PETIOLE (BOP) transcriptional cofactors, defined by the conserved BTB (Broad complex, Tramtrack, and Bric-a-brac)/POZ (POX virus and zinc finger) domain. TMF and three tomato BOPs (SlBOPs) interact with themselves and each other, and TMF recruits SlBOPs to the nucleus, suggesting formation of a transcriptional complex. Like TMF, SlBOP gene expression is highest during vegetative and transitional stages of meristem maturation, and CRISPR/Cas9 elimination of SlBOP function causes pleiotropic defects, most notably simplification of inflorescences into single flowers, resembling tmf mutants. Flowering defects are enhanced in higher-order slbop tmf mutants, suggesting that SlBOPs function with additional factors. In support of this, SlBOPs interact with TMF homologs, mutations in which cause phenotypes like slbop mutants. Our findings reveal a new flowering module defined by SlBOP–TMF family interactions that ensures a progressive meristem maturation to promote inflorescence complexity.

Genome-wide association analyses of 54 traits identified multiple loci for the determination of floret fertility in wheat

Increasing grain yield is still the main target of wheat breeding; yet today's wheat plants utilize less than half of their yield potential. Owing to the difficulty of determining grain yield potential in a large population, few genetic factors regulating floret fertility (i.e. the difference between grain yield potential and grain number) have been reported to date. In this study, we conducted a genome-wide association study (GWAS) by quantifying 54 traits (16 floret fertility traits and 38 traits for assimilate partitioning and spike morphology) in 210 European winter wheat accessions. The results of this GWAS experiment suggested potential associations between floret fertility, assimilate partitioning and spike morphology revealed by shared quantitative trait loci (QTLs). Several candidate genes involved in carbohydrate metabolism, phytohormones or floral development colocalized with such QTLs, thereby providing potential targets for selection. Based on our GWAS results we propose a genetic network underlying floret fertility and related traits, nominating determinants for improved yield performance.

Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley

Background

Barley semi-dwarf genes have been extensively explored and widely used in barley breeding programs. The semi-dwarf gene ari-e from Golden Promise is an important gene associated with some agronomic traits and salt tolerance. While ari-e has been mapped on barley chromosome 5H using traditional markers and next-generation sequencing technologies, it has not yet been finely located on this chromosome.

Results

We integrated two methods to develop molecular markers for fine-mapping the semi-dwarf gene ari-e: (1) specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to develop SNP markers, and (2) the whole-genome shotgun sequence to develop InDels. Both SNP and InDel markers were developed in the target region and used for fine-mapping the ari-e gene. Linkage analysis showed that ari-e co-segregated with marker InDel-17 and was delimited by two markers (InDel-16 and DGSNP21) spanning 6.8 cM in the doubled haploid (DH) Dash × VB9104 population. The genetic position of ari-e was further confirmed in the Hindmarsh × W1 DH population which was located between InDel-7 and InDel-17. As a result, the overlapping region of the two mapping populations flanked by InDel-16 and InDel-17 was defined as the candidate region spanning 0.58 Mb on the POPSEQ physical map.

Conclusions

The current study demonstrated the SLAF-seq for SNP discovery and whole-genome shotgun sequencing for InDel development as an efficient approach to map complex genomic region for isolation of functional gene. The ari-e gene was fine mapped from 10 Mb to 0.58 Mb interval.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3247-4) contains supplementary material, which is available to authorized users.

The Genetic Architecture of Barley Plant Stature

Plant stature in temperate cereals is predominantly controlled by tillering and plant height as complex agronomic traits, representing important determinants of grain yield. This study was designed to reveal the genetic basis of tillering at five developmental stages and plant height at harvest in 218 worldwide spring barley (Hordeum vulgare L.) accessions under greenhouse conditions. The accessions were structured based on row-type classes [two- vs. six-rowed] and photoperiod response [photoperiod-sensitive (Ppd-H1) vs. reduced photoperiod sensitivity (ppd-H1)]. Phenotypic analyses of both factors revealed profound between group effects on tiller development. To further verify the row-type effect on the studied traits, Six-rowed spike 1 (vrs1) mutants and their two-rowed progenitors were examined for tiller number per plant and plant height. Here, wild-type (Vrs1) plants were significantly taller and had more tillers than mutants suggesting a negative pleiotropic effect of this row-type locus on both traits. Our genome-wide association scans further revealed highly significant associations, thereby establishing a link between the genetic control of row-type, heading time, tillering, and plant height. We further show that associations for tillering and plant height are co-localized with chromosomal segments harboring known plant stature-related phytohormone and sugar-related genes. This work demonstrates the feasibility of the GWAS approach for identifying putative candidate genes for improving plant architecture.

A Homolog of Blade-On-Petiole 1 and 2 (BOP1/2) Controls Internode Length and Homeotic Changes of the Barley Inflorescence

Inflorescence architecture in small-grain cereals has a direct effect on yield and is an important selection target in breeding for yield improvement. We analyzed the recessive mutation laxatum-a (lax-a) in barley (Hordeum vulgare), which causes pleiotropic changes in spike development, resulting in (1) extended rachis internodes conferring a more relaxed inflorescence, (2) broadened base of the lemma awns, (3) thinner grains that are largely exposed due to reduced marginal growth of the palea and lemma, and (4) and homeotic conversion of lodicules into two stamenoid structures. Map-based cloning enforced by mapping-by-sequencing of the mutant lax-a locus enabled the identification of a homolog of BLADE-ON-PETIOLE1 (BOP1) and BOP2 as the causal gene. Interestingly, the recently identified barley uniculme4 gene also is a BOP1/2 homolog and has been shown to regulate tillering and leaf sheath development. While the Arabidopsis (Arabidopsis thaliana) BOP1 and BOP2 genes act redundantly, the barley genes contribute independent effects in specifying the developmental growth of vegetative and reproductive organs, respectively. Analysis of natural genetic diversity revealed strikingly different haplotype diversity for the two paralogous barley genes, likely affected by the respective genomic environments, since no indication for an active selection process was detected.

Identification and validation of novel low-tiller number QTL in common wheat

SNP-based QTL mapping provided useful information for novel loci that can be used in breeding programs to control tillering and improve yield in wheat via marker-assisted selection. Tillering is one of the most important agronomic traits affecting biomass and grain yield potential in wheat. Wheat lines with very limited tillering capacity are more productive than free-tillering lines under severe drought conditions. In this study, three recombinant inbred line (RIL) populations were generated and used, having H461, a low-tillering genotype, as a common parent. A linkage map containing 7808 single nucleotide polymorphism loci was constructed on the basis of H461/CN16 RIL population. Three QTL controlling low tillering were identified on Chromosome (Chr.) 2D (Qltn.sicau-2D), Chr. 2B (Qltn.sicau-2B), and Chr. 5A (Qltn.sicau-5A). Qltn.sicau-2D, Qltn.sicau-2B, and Qltn.sicau-5A explained up to 19.1, 14.6, and 9.6 % of the phenotypic variance, respectively. Comparing with previous findings, Qltn.sicau-2D and Qltn.sicau-2B should thus be novel tillering QTL. The effects of these QTL were further validated in two additional RIL populations. Significant effects of Qltn.sicau-2D were detected across all growth stages in different genetic backgrounds, making it an ideal target for breeding programs as well as for further characterization of the gene(s) underlying this locus.

Keep on growing: building and patterning leaves in the grasses

Monocot leaves have unique features that arise early in their development. Maturing leaves protectively enclose younger leaves and the meristem, the pool of founder cells from which a leaf emerges. Through the maturation process, proximal sheath and distal blade tissues differentiate and are separated by the ligule and auricle structures. Here we review current research focusing on the contribution of gene regulatory factors and phytohormones on the patterning and differentiation of monocot leaves primarily focusing on research in the grasses (Poaceae). The 10000 members of the grasses include the true grain cereals (wheat, rice, maize, etc.), biofuel crops such as sugarcane, pasture grasses, and bamboo. They are the most studied of the monocots due to their tremendous agricultural and agronomic importance.

Divide et impera: boundaries shape the plant body and initiate new meristems

485 I. 485 II. 486 III. 491 IV. 491 V. 495 495 References 495 SUMMARY: Boundaries, established and maintained in different regions of the plant body, have diverse functions in development. One role is to separate different cell groups, for example the differentiating cells of a leaf primordium from the pluripotent cells of the apical meristem. Boundary zones are also established during compound leaf development, to separate young leaflets from each other, and in many other positions of the plant body. Recent studies have demonstrated that different boundary zones share similar properties. They are characterized by a low rate of cell divisions and specific patterns of gene expression. In addition, the levels of the plant hormones auxin and brassinosteroids are down-regulated in boundary zones, resulting in a low differentiation level of boundary cells. This feature seems to be crucial for a second important role of boundary zones, the formation of new meristems. The primary shoot meristem, as well as secondary and ectopic shoot meristems, initiate from boundary cells that exhibit competence for meristem formation.

The legume NOOT-BOP-COCH-LIKE genes are conserved regulators of abscission, a major agronomical trait in cultivated crops

Plants are able to lose organs selectively through a process called abscission. This process relies on the differentiation of specialized territories at the junction between organs and the plant body that are called abscission zones (AZ). Several genes control the formation or functioning of these AZ. We have characterized BLADE-ON-PETIOLE (BOP) orthologues from several legume plants and studied their roles in the abscission process using a mutant approach. Here, we show that the Medicago truncatula NODULE ROOT (NOOT), the Pisum sativum COCHLEATA (COCH) and their orthologue in Lotus japonicus are strictly necessary for the abscission of not only petals, but also leaflets, leaves and fruits. We also showed that the expression pattern of the M. truncatula pNOOT::GUS fusion is associated with functional and vestigial AZs when expressed in Arabidopsis. In addition, we show that the stip mutant from Lupinus angustifolius, defective in stipule formation and leaf abscission, is mutated in a BOP orthologue. In conclusion, this study shows that this clade of proteins plays an important conserved role in promoting abscission of all aerial organs studied so far.

Beyond the Divide: Boundaries for Patterning and Stem Cell Regulation in Plants

The initiation of plant lateral organs from the shoot apical meristem (SAM) is closely associated with the formation of specialized domains of restricted growth known as the boundaries. These zones are required in separating the meristem from the growing primordia or adjacent organs but play a much broader role in regulating stem cell activity and shoot patterning. Studies have revealed a network of genes and hormone pathways that establish and maintain boundaries between the SAM and leaves. Recruitment of these pathways is shown to underlie a variety of processes during the reproductive phase including axillary meristems production, flower patterning, fruit development, and organ abscission. This review summarizes the role of conserved gene modules in patterning boundaries throughout the life cycle.