Biology subjects

Koppolu, R.

Publications and source records attributed to Koppolu, R..

8 recordsLinked to original sources

bioRxiv2026

Rate of meristem initiation driven by the MADS-WUS axis contributes to floral survival and inflorescence evolution in grasses

Crop domestication has repeatedly shaped inflorescence architecture to improve floral production, but mechanisms coordinating the rate of floral initiation, maturation and survival remain unclear. Combining morphometry, modelling and molecular genetic analyses, we show that floral production in the indeterminate barley (Hordeum vulgare L.) inflorescence follows an "initiate fast-die young" strategy orchestrated by a main MADS-box gene, SPIKELET INITIATION AND FERTILITY (SIF). SIF accomplishes this duality by coordinately terminating the inflorescence meristem via WUSCHEL and activating the floral meristem via APETALA1 (Vrn-H1). Hereby, the ancestral SIF "slow" allele promotes a timely commitment to floral maturation, whereas the derived "fast" allele permits more floral initiations. Postdomestication selection of SIF alleles thus enables diversified reproductive strategies in barley populations to maintain yield traits in the field. Finally, we show that a lineage-specific SIF duplication contributed to meristem fate transition and inflorescence evolution during Triticeae cold adaptation. Our results establish developmental rate as a key driver of architectural innovation and reproductive success.

plant biology↗

bioRxiv2024

Adaptive diversification through structural variation in barley

Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here, we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that have become hot spots of gene copy number variation in evolutionarily recent times. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release, and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that rapid evolution at structurally complex loci may have helped crop plants adapt to new selective regimes in agricultural ecosystems.

plant biology↗

bioRxiv2023

Anatomical insights into the vascular lay-out of the barley rachis: implications for transport and spikelet connection

Background and aimsVascular patterning is intimately related to plant form and function. However, morphologic a l studies on the vascular anatomy of cereal crops, and inflorescences in particular, are scarce despite their importance for grain yield determination. Here, using barley (Hordeum vulgare) as a model, we study the vascular anatomy of the spike-type inflorescence. Our goal is to clarify the relationship between rachis (spike axis) vasculature and spike size, the implications for transport capacity and its interaction with the spikelets. MethodsWe employed serial transversal internode sections in multiple barley lines with different spike size, and investigated the internode diameter, vascular area and vein number size along the mature barley rachis. We then modeled the vascular dynamics along the main spike axis, and analyzed their relationship with spike size. Key resultsInternode diameter and total vascular area have a clear positive correlation with spike size whereas vascular number is only weakly correlated. While the lateral periphery of the rachis contains large mature veins of constant diameter the central part is occupied by a staggered array of small immature veins. This underlines the importance of minimizing transport resistance and suggests that transport and distribution of nutrients are spatially separated. Spikelet-derived veins enter the rachis either in the central area, where they often merge with the immature rachis veins, or in the periphery where they do not merge with the large mature veins. An increase in floret fertility through the conversion of a two-rowed barley into an isogenic six-rowed line, as well a decrease in floret fertility due to enhanced pre-anthesis tip degeneration caused by the mutation tip sterile 2.b (tst2.b) significantly affected vein size, but had limited to no effects on vein number or rachis diameter. Comparative analysis of a wild barley accession suggests that the domestication of barley may have favored plants with enhanced rachis transport capacity. ConclusionsThe rachis vasculature is the result of a two-step process involving an initial lay-out followed by size adjustment according to floret fertility/spike size. The functional processes of long distance transport and local supply to spikelets are spatially separated while a vascular continuity between rachis and spikelets appears non-essential.

plant biology↗

bioRxiv2021

Dosage of duplicated and antifunctionalized homeobox proteins influences spikelet development in barley

Illuminating the mechanisms of inflorescence architecture of grain crops that feed our world may strengthen the goal towards sustainable agriculture. Lateral spikelet development of barley (Hordeum vulgare L.) is such an example of a floral architectural trait regulated by VRS1 (Vulgare Row-type Spike 1 or Six-rowed Spike 1, syn. HvHOX1). Its lateral spikelet-specific expression and the quantitative nature of suppressing spikelet development were previously shown in barley. However, the mechanistic function of this gene and its paralog HvHOX2 on spikelet development is still fragmentary.Here, we show that these duplicated transcription factors (TFs) have contrasting nucleotide diversity in various barley genotypes and several Hordeum species. Despite this difference, both proteins retain their basic properties of the homeodomain leucine zipper class I family of TFs. During spikelet development, these genes exhibit similar spatiotemporal expression patterns yet with anticyclic expression levels. A gene co-expression network analysis suggested that both have an ancestral relationship but their functions appear antagonistic to each other, i.e., HvHOX1 suppresses whereas HvHOX2 rather promotes spikelet development. Our transgenic promoter-swap analysis showed that HvHOX2 can restore suppressed lateral spikelets when expression levels are increased; however, at its low endogenous expression level, HvHOX2 appears dispensable for spikelet development. Collectively, this study proposes that the dosage of the two antagonistic TFs, HvHOX1 and HvHOX2, influence spikelet development in barley.

plant biology↗

bioRxiv2021

The barley mutant multiflorus2.b reveals quantitative genetic variation for new spikelet architecture

Understanding the genetic basis of yield forming factors in small grain cereals is of extreme importance, especially in the wake of stagnation of further yield gains in these crops. One such yield forming factor in these cereals is the number of grain-bearing florets produced per spikelet. Wildtype barley (Hordeum vulgare L.) spikelets are determinate structures, the spikelet axis (rachilla) degenerates after producing single floret. In contrast, the rachilla of wheat (Triticum ssp.) spikelets, which are indeterminate, elongates to produce up to 12 florets. In our study, we characterized the barley spikelet determinacy mutant multiflorus2.b (mul2.b) that produced up to three fertile florets on elongated rachillae of lateral spikelets. Apart from the lateral spikelet indeterminacy (LS-IN), we also characterized the supernumerary spikelet phenotype in the central spikelets (CS-SS) of mul2.b. Through our phenotypic and genetic analyses, we identified two major QTLs on chromosomes 2H and 6H, and two minor QTLs on 3H for the LS-IN phenotype. For, the CS-SS phenotype we identified one major QTL on 6H, and a minor QTL on 5H chromosomes. Notably, the 6H QTLs for CS-SS and LS-IN phenotypes co-located with each other, potentially indicating that a single genetic factor might regulate both phenotypes. Thus, our in-depth phenotyping combined with genetic analyses revealed the quantitative nature of the LS-IN and CS-SS phenotypes in mul2.b, paving the way for cloning the genes underlying these QTLs in the future. Key messageSpikelet indeterminacy and supernumerary spikelet phenotypes in barley multiflorus2.b mutant show polygenic inheritance. Genetic analysis of multiflorus2.b revealed major QTLs for spikelet determinacy and supernumerary spikelet phenotypes on 2H and 6H chromosomes.

plant biology↗

bioRxiv2020

Modes of grain number determination differentiate barley row-types

Gaining knowledge on intrinsic interactions of various yield components is crucial to improve the yield potential in small grain cereals. It is well known in barley that increasing the grain number (GN) preponderantly improves their yield potential; however, the yield components determining GN and their association in barley row-types are less explored. In this study, we assessed different yield components like potential spikelet number (PSN), spikelet survival (SSL), spikelet number (SN), grain set (GS), and grain survival (GSL), as well as their interactions with GN by using a selected panel of two- and six-rowed barley types. Also, to analyze the stability of these interactions, we performed the study in two growth conditions, greenhouse and field. From this study, we found that in two-rowed, GN determination is strongly influenced by PSN rather than SSL and/or GS in both growth conditions. Conversely, in six-rowed, GN is associated with SSL instead of PSN and/or GS. Thus, our study exemplified that increasing GN might be possible by augmenting PSN in two-rowed genotypes, while for six-rowed genotypes, the ability of SSL needs to be improved. We speculate that this disparity of GN determination in barley row-types might be due to the fertility of lateral spikelets. Collectively, this study revealed that the GN of two-rowed largely depends on the developmental trait, PSN, while in six-rowed, it mainly follows the ability of SSL. HighlightIn cereals, understanding the interactions of different yield components that influence the grain number is essential to increase their yield by modulating the components. We show in this study that the grain number of two-rowed barley is predominantly determined by the potential spikelet number while in six-rowed by spikelet survival.

plant biology↗

bioRxiv2020

COMPOSITUM 1 (COM1) contributes to the architectural simplification of barley inflorescence via cell wall-mediated and meristem identity signals

Grasses have varying inflorescence shapes; however, little is known about the genetic mechanisms specifying such shapes among tribes. We identified the grass-specific TCP transcription factor COMPOSITUM 1 (COM1) expressed in inflorescence meristematic boundaries of different grasses. COM1 specifies branch-inhibition in Triticeae (barley) versus branch-formation in non-Triticeae grasses. Analyses of cell size, cell walls and transcripts revealed barley COM1 regulates cell growth, affecting cell wall properties and signaling specifically in meristematic boundaries to establish identity of adjacent meristems. COM1 acts upstream of the boundary gene Liguleless1 and confers meristem identity partially independent of the COM2 pathway. Furthermore, COM1 is subject to purifying natural selection, thereby contributing to specification of the spike inflorescence shape. This meristem identity pathway has conceptual implications for both inflorescence evolution and molecular breeding in Triticeae.

plant biology↗

bioRxiv2019

TaAPO-A1, an ortholog of rice ABERRANT PANICLE ORGANIZATION 1, is associated with total spikelet number per spike in elite hexaploid winter wheat varieties (Triticum aestivum L.)

We dissected the genetic basis of total spikelet number (TSN) along with other traits, namely spike length (SL) and flowering time (FT) in a panel of 518 elite European winter wheat varieties. Genome-wide association studies based on 39,908 SNP markers revealed highly significant quantitative trait loci (QTL) for TSN on chromosomes 2D, 7A, and 7B, for SL on 5A, and FT on 2D, with 2D-QTL being the functional marker for the gene Ppd-D1. The physical region of the 7A-QTL for TSN revealed the presence of an ortholog to APO1 - a rice gene that positively controls spikelet number on panicles. Interspecific analyses of TaAPO-A1 orthologs showed that it is a highly conserved gene important for floral development, and present in a wide range of terrestrial plants. Intraspecific studies of the wheat ortholog TaAPO-A1 across wheat genotypes revealed a polymorphism in the highly conserved F-box domain, defining two haplotypes. A KASP maker developed on the polymorphic site showed a highly significant association of TaAPO-A1 with TSN, explaining 23.2% of the genotypic variance. Also, the TaAPO-A1 alleles showed weak but significant differences for SL and grain yield. Our results demonstrate the importance of wheat sequence resources to identify candidate genes for important traits based on genetic analyses.

genetics↗