In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris (L)., the major locus qPD5.1-Pv for pod indehiscence was identified recently. We developed a BC4/F4 introgression line population and narrowed the major locus down to a 22.5-kb region. Here, gene expression and a parallel histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest associated peak. Based on mapping and expression data, we propose early and fine up-regulation of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is associated to the lack of a functional abscission layer in the ventral sheath, and that the key anatomical modifications associated with pod shattering in common bean occur early during pod development. We finally propose that loss of pod shattering in legumes resulted from histological convergent evolution and that it is the result of selection at orthologous loci.

To elucidate the physiology underlying the development of superficial scald in pears, susceptible "Blanquilla" fruit was treated with different compounds that either promoted (ethylene) or repressed (1-methylcyclopropene and lovastatin) the incidence of this disorder after 4 months of cold storage. Our data show that scald was negligible for the fruit treated with 1-methylcyclopropene or lovastatin, but highly manifested in untreated (78% incidence) or ethylenetreated fruit (97% incidence). The comparison between the fruit metabolomic profile and transcriptome evidenced a distinct reprogramming associated with each treatment. In all treated samples, cold storage led to an activation of a cold-acclimation-resistance mechanism, including the biosynthesis of very-long-chain fatty acids, which was especially evident in 1-methylcyclopropane-treated fruit. Among the treatments applied, only 1-methylcyclopropene inhibited ethylene production, hence supporting the involvement of this hormone in the development of scald. However, a common repression effect on the PPO gene combined with higher sorbitol content was found for both lovastatin and 1-methylcyclopropene-treated samples, suggesting also a non-ethylene-mediated process preventing the development of this disorder. The results presented in this work represent a step forward to better understand the physiological mechanisms governing the etiology of superficial scald in pears.

Eukaryotic genomes are pervasively transcribed and only a small portion of the transcribed sequences belongs to protein coding genes. High-throughput sequencing technology contributed to consolidate this perspective, allowing the identification of numerous noncoding RNAs with key roles in biological processes. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nt with limited phylogenetic conservation, expressed at low levels and characterized by tissue/organ specific expression profiles. Although a large set of lncRNAs has been identified, the functional roles of lncRNAs are only beginning to be recognized and the molecular mechanism of lncRNA-mediated gene regulation remains largely unexplored, particularly in plants where their annotation and characterization are still incomplete. Using public and proprietary poly-(A)+ RNA-seq data as well as a collection of full length ESTs from several organs, developmental stages and stress conditions in three Brachypodium distachyon inbred lines, we describe the identification and the main features of thousands lncRNAs. Here we provide a genome-wide characterization of lncRNAs, highlighting their intraspecies conservation and describing their expression patterns among several organs/tissues and stress conditions. This work represents a fundamental resource to deepen our knowledge on long noncoding RNAs in C3 cereals, allowing the Brachypodium community to exploit these results in future research programs.

Short title:The pod-shattering syndrome in common bean 32 33 One-sentence summary: A non-functional abscission layer determines the loss of pod 34 shattering; mapping data, and parallel gene expression and histological analysis support 35 PvMYB26 as the candidate gene for pod indehiscence.36 37The author responsible for distribution of materials integral to the findings presented in this 38 article in accordance with the policy described in the Instructions for Authors 39 (www.plantcell.org) is: Roberto Papa (r.papa@univpm.it). 40 41 42 2 43 ABSTRACT 44In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment 45 of the valves promotes seed dispersal. In Phaseolus vulgaris, the major locus qPD5.1-Pv for pod 46 indehiscence was identified recently. We developed a BC4/F4 introgression line population and 47 narrowed the major locus down to a 22.5-kb region. Here, gene expression and a parallel 48 histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the 49 best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest 50 associated peak. Based on mapping and expression data, we propose early and fine up-regulation 51 of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is 52 associated to the lack of a functional abscission layer in the ventral sheath, and that the key 53 anatomical modifications associated with pod shattering in common bean occur early during pod 54 development. We finally propose that loss of pod shattering in legumes resulted from histological 55 convergent evolution and that this is the result of selection at orthologous loci. 56 57 58 Keywords: pod shattering, common bean, MYB26, genome-wide association study, gene 59 expression, pod anatomy, convergent evolution, introgression lines.60 61 62 63 Loss of seed shattering is a paradigmatic example of the changes that have occurred to crop plant 64 traits compared to their wild progenitors, which collectively constitute the 'domestication 65 syndrome' (Hammer 1984). In wild species, specialised seed-dispersal strategies are of 66 fundamental importance for plant survival and fitness. Conversely, in domesticated forms, loss or 67 reduction of seed shattering is desired to reduce yield losses. 68 Due to its complex evolutionary history, common bean (Phaseolus vulgaris L.) is an 69 excellent model to study the domestication process (Bitocchi et al., 2017), which included its 70 parallel domestication in the Andes and Mesoamerica (Bitocchi et al., 2013). In P. vulgaris, the 71 dry beans are characterised by different degrees of pod shattering. These represent the majority of 72 the domesticated pool (Gepts and Debouck 1991), where a limited level of pod shattering has 73 been conserved to favour the threshing of the dry pods. Variations in the pod shattering intensity 74 are also associated with the environmental conditions during maturation (e.g., humidity and 75 temperature) (Parker et al., 2020). 76 ...

Recent advances in high throughput sequencing technology have revealed a pervasive and complex transcriptional activity of all eukaryotic genomes and have allowed the identification and characterization of several classes of noncoding RNAs (ncRNAs) with key roles in various biological processes. Among ncRNAs, long ncRNAs (lncRNAs) are transcripts typically longer than 200 nucleotides whose members tend to be expressed at low levels, show a lack of phylogenetic conservation and exhibit tissue-specific, cell-specific, or stress-responsive expression profiles.Although a large set of lncRNAs has been identified both in animal and plant systems, the regulatory roles of lncRNAs are only beginning to be recognized and the molecular basis of lncRNA mediated gene regulation remains largely unexplored, particularly in plants.Here, we describe an efficient methodology to identify long noncoding RNAs using next-generation sequencing data.