Loss of pod strings in common bean is associated with gene duplication, retrotransposon insertion, and overexpression of PvIND

Regulation of fruit development has been central in the evolution and domestication of flowering plants. In common bean (Phaseolus vulgaris L.), a major global staple crop, the two main economic categories are distinguished by differences in fiber deposition in pods: a)dry beans with fibrous and stringy pods; and b) stringless snap/green beans withreduced fiber deposition, but which frequently revert to the ancestral stringy state. To better understand control of this important trait, we first characterized developmental patterns of gene expression in four phenotypically diverse varieties. Then, using isogenic stringless/revertant pairs of six snap bean varieties, we identified strong overexpression of the common bean ortholog of INDEHISCENT (PvIND) in non-stringy types compared to their string-producing counterparts. Microscopy of these pairs indicates that PvIND overexpression is associated with overspecification of weak dehiscence zone cells throughout the entire pod vascular sheath. No differences in PvIND DNA methylation were correlated with pod string phenotype. Sequencing of a 500 kb region surrounding PvIND in the stringless snap bean cultivar Hystyle revealed that PvIND had been duplicated into two tandem repeats, and that a Ty1-copia retrotransposon was inserted between these tandem repeats, possibly driving PvIND overexpression. Further sequencing of stringless/revertant isogenic pairs and diverse materials indicated that these sequence features had been uniformly lost in revertant types and were strongly predictive of pod phenotype, supporting their role in PvIND overexpression and pod string phenotype.

Shattering tolerance in Brassica napus L.

Brassica is the second-largest oilseed crop after Soybean. The total production of Brassica in the overall world is 71 million tons. In Pakistan, its total production per unit area is very low. Biotic and abiotic stresses mainly affect the brassica crop. In agriculture, shattering is the dispersal of crops seeds before their ripening. The pod wall shatters and breaks apart when it loses its hydration and cells split in a dehiscence zone organized at a suture between the edge of the lignified pod and the vascular tissue replum. The degeneration of middle lamella and loss of cellular cohesion in the dehiscence zone are the main reasons for pod shattering and seed losses. Grain yield losses in Brassica vary from 10 to 25 percent due to shattering. More than 400 kg has-1 or 12% seed losses can be occurred due to pod shattering under unfavorable conditions. Insect pest and disease damage also accelerate ripening and pod shattering. The main breeding techniques for developing rapeseed grain yield potential are a good knowledge and application of the morphological, physiological, and genetic basis of grain yield. Modern technologies, such as embryo rescue, marker-assisted breeding, and novel variation (mutation), may make it much simpler to introduce new rapeseed types having shattering tolerance than traditional methods. Thus, an overview of anatomical and physiological aspects and genetics of shattering is presented in the context of recent advances in molecular genetics and several agronomic managements to avoid shattering in Brassica.

INDEHISCENT regulates explosive seed dispersal

How traits evolve to produce novelty or stasis is an open question in biology. We investigate this question in Cardamine hirsuta, a relative of Arabidopsis thaliana that employs explosive fracture to disperse its seeds. This trait evolved through key morphomechanical innovations that distinguish the otherwise very similar, dehiscent fruit of these two species. Using CRISPR/Cas9, we show that dehiscence zone formation is absolutely required for explosive fracture in C. hirsuta, and is controlled by the bHLH transcription factor INDEHISCENT (IND). Using mutant screens, we identified the MADS-box transcription factor FRUITFULL (FUL) as a negative regulator of IND in C. hirsuta. Although FUL function is conserved in C. hirsuta, the consequences of IND mis-expression differ in ful mutants of C. hirsuta versus A. thaliana. In ful mutants of both species, valve tissue is replaced by dehiscence zone tissue, which comprises two distinct cell types: lignified layer and separation layer cells. While A. thaliana ful mutants develop stunted fruit with ectopic lignified layer cells, C. hirsuta ful mutants have elongated fruit with ectopic separation layer cells. We show that IND dose determines the proportion of these two cell types in ectopic dehiscence zones. We also show that the extent of ectopic lignification caused by IND mis-expression determines fruit length. Our findings indicate developmental system drift in the conserved gene network patterning dehiscent fruit in two related Brassicaceae species.

Pod Shattering in Grain Legumes: Emerging Genetic and Environment-Related Patterns

A reduction in pod shattering is one of the main components of grain legume domestication. Despite this, many domesticated legumes suffer serious yield losses due to shattering, particularly under arid conditions. Mutations related to pod shattering modify the twisting force of pod walls or the structural strength of the dehiscence zone in pod sutures. At a molecular level, a growing body of evidence indicates that these changes are controlled by a relatively small number of key genes that have been selected in parallel across grain legume species, supporting partial molecular convergence. Legume homologues of Arabidopsis thaliana silique shattering genes play only minor roles in legume pod shattering. Most domesticated grain legume species contain multiple shattering-resistance genes, with mutants of each gene typically showing only partial shattering resistance. Hence, crosses between varieties with different genes lead to transgressive segregation of shattering alleles, producing plants with either enhanced shattering resistance or atavistic susceptibility to the trait. The frequency of these resistance pod-shattering alleles is often positively correlated with environmental aridity. The continued development of pod-shattering-related functional information will be vital for breeding crops that are suited to the increasingly arid conditions expected in the coming decades.

First approach to pod dehiscence in faba bean: genetic and histological analyses

Pod dehiscence causes important yield losses in cultivated crops and therefore has been a key trait strongly selected against in crop domestication. In spite of the growing knowledge on the genetic basis of dehiscence in different crops, no information is available so far for faba bean. Here we conduct the first comprehensive study for faba bean pod dehiscence by combining, linkage mapping, comparative genomics, QTL analysis and histological examination of mature pods. Mapping of dehiscence-related genes revealed conservation of syntenic blocks among different legumes. Three QTLs were identified in faba bean chromosomes II, IV and VI, although none of them was stable across years. Histological analysis supports the convergent phenotypic evolution previously reported in cereals and related legume species but revealed a more complex pattern in faba bean. Contrary to common bean and soybean, the faba bean dehiscence zone appears to show functional equivalence to that described in crucifers. The lignified wall fiber layer, which is absent in the paucijuga primitive line Vf27, or less lignified and vacuolated in other dehiscent lines, appears to act as the major force triggering pod dehiscence in this species. While our findings, provide new insight into the mechanisms underlying faba bean dehiscence, full understanding of the molecular bases will require further studies combining precise phenotyping with genomic analysis.

ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) releases latent defense signals in stems with reduced lignin content

There is considerable interest in engineering plant cell wall components, particularly lignin, to improve forage quality and biomass properties for processing to fuels and bioproducts. However, modifying lignin content and/or composition in transgenic plants through down-regulation of lignin biosynthetic enzymes can induce expression of defense response genes in the absence of biotic or abiotic stress. Arabidopsis thaliana lines with altered lignin through down-regulation of hydroxycinnamoyl CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT) or loss of function of cinnamoyl CoA reductase 1 (CCR1) express a suite of pathogenesis-related (PR) protein genes. The plants also exhibit extensive cell wall remodeling associated with induction of multiple cell wall-degrading enzymes, a process which renders the corresponding biomass a substrate for growth of the cellulolytic thermophile Caldicellulosiruptor bescii lacking a functional pectinase gene cluster. The cell wall remodeling also results in the release of size- and charge-heterogeneous pectic oligosaccharide elicitors of PR gene expression. Genetic analysis shows that both in planta PR gene expression and release of elicitors are the result of ectopic expression in xylem of the gene ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1), which is normally expressed during anther and silique dehiscence. These data highlight the importance of pectin in cell wall integrity and the value of lignin modification as a tool to interrogate the informational content of plant cell walls.

A plant biostimulant from the seaweed Ascophyllum nodosum (Sealicit) reduces podshatter and yield loss in oilseed rape through modulation of IND expression

The yield of podded crops such as oilseed rape (OSR) is limited by evolutionary adaptations of the plants for more efficient and successful seed dispersal for survival. These plants have evolved dehiscent dry fruits that shatter along a specifically developed junction at carpel margins. A number of strategies such as pod sealants, GMOs and hybrids have been developed to mitigate the impact of pod shatter on crop yield with limited success. Plant biostimulants have been shown to influence plant development. A challenge in plant biostimulant research is elucidating the mechanisms of action. Here we have focused on understanding the effect of an Ascophyllum nodosum based biostimulant (Sealicit) on fruit development and seed dispersal trait in Arabidopsis and OSR at genetic and physiological level. The results indicate that Sealicit is affecting the expression of the major regulator of pod shattering, INDEHISCENT, as well as disrupting the auxin minimum. Both factors influence the formation of the dehiscence zone and consequently reduce pod shattering. Unravelling the mode of action of this unique biostimulant provides data to support its effectiveness in reducing pod shatter and highlights its potential for growers to increase seed yield in a number of OSR varieties.

Physiological and molecular aspects of pod shattering resistance in crops

Pod shattering resistance is a trait acquired by crops in the process of evolution. Manipulation of physiological and molecular processes is fundamental for the improvement of shattering resistance in crops. In this review we discuss several enzymes, key hormones and their possible roles or relationships involved in pod shattering, and highlight responsible genes, quantitative traits loci (QTLs) and their implications for increased pod shattering resistance. Cell wall degrading enzymes, particularly β-glucanases and endopolygalacturonases play an important role in the process of pod dehiscence. It is not clear how and to what extent a specific hormone regulates the dehiscence zone differentiation and the dehiscence process is not clear. Resistance to shattering is highly heritable and is not controlled by a single gene. Several QTLs associated to dehiscence have been identified in crops, while the underlying genetic functions of these QTLs deserve further investigation. Further physiological analyses of the pod wall will help to understand better the pod dehiscence.