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SUMMARY The repeated evolution of high seed shattering during multiple independent de‐domestications of cultivated Asian rice (Oryza sativa) into weedy rice (Oryzaspp.) is a prime example of convergent evolution. Weedy rice populations converge in histological features of the abscission zone (AZ), a crucial structure for seed abscission, while ancestral cultivated rice populations exhibit varied AZ morphology and levels of shattering. However, the genetic bases of these phenotypic patterns remain unclear. We examined the expression profiles of the AZ region and its surrounding tissues at three developmental stages in two low‐shattering cultivars ofausandtemperate japonicadomesticated groups and in two genotypes of their derived high‐shattering weed groups, Blackhull Awned (BHA) and Spanish Weedy Rice (SWR), respectively. Consistent with the greater alteration of AZ morphology during the de‐domestication of SWR than BHA, fewer genes exhibited a comparable AZ‐region exclusive expression pattern between weed and crop in thetemperate japonicalineage than in theauslineage. Transcription factors related to the repression of lignin and secondary cell wall deposition, such as,OsWRKY102andOsXND‐1‐like, along with certain known shattering genes involved in AZ formation, likely played a role in maintaining AZ region identity in both lineages. Meanwhile, most genes exhibiting AZ‐region exclusive expression patterns do not overlap between the two lineages and the genes exhibiting differential expression in the AZ region between weed and crop across the two lineages are enriched for different gene ontology terms. Our findings suggest genetic flexibility in shaping AZ morphology, while genetic constraints on AZ identity determination in these two lineages. 

Abstract The modification of seed shattering has been a recurring theme in rice evolution. The wild ancestor of cultivated rice disperses its seeds, but reduced shattering was selected during multiple domestication events to facilitate harvesting. Conversely, selection for increased shattering occurred during the evolution of weedy rice, a weed invading cultivated rice fields that has originated multiple times from domesticated ancestors. Shattering requires formation of a tissue known as the abscission zone (AZ), but how the AZ has been modified throughout rice evolution is unclear. We quantitatively characterized the AZ characteristics of relative length, discontinuity, and intensity in 86 cultivated and weedy rice accessions. We reconstructed AZ evolutionary trajectories and determined the degree of convergence among different cultivated varieties and among independent weedy rice populations. AZ relative length emerged as the best feature to distinguish high and low shattering rice. Cultivated varieties differed in average AZ morphology, revealing lack of convergence in how shattering reduction was achieved during domestication. In contrast, weedy rice populations typically converged on complete AZs, irrespective of origin. By examining AZ population-level morphology, our study reveals its evolutionary plasticity, and suggests that the genetic potential to modify the ecologically and agronomically important trait of shattering is plentiful in rice lineages. 

Abstract PremiseThe scents of volatile organic compounds (VOCs) are an important component of ripe fleshy fruit attractiveness, yet their variation across closely related wild species is poorly understood. Phylogenetic patterns in these compounds and their biosynthetic pathways offer insight into the evolutionary drivers of fruit diversity, including whether scent can communicate an honest signal of nutrient content to animal dispersers. We assessed ripe fruit VOC content across the tomato clade (Solanumsect.Lycopersicon), with implications for crop improvement since these compounds are key components of tomato flavor. MethodsWe analyzed ripe fruit volatiles from 13 species of wild tomato grown in a common garden. Interspecific variations in 66 compounds and their biosynthetic pathways were assessed in 32 accessions, and an accession‐level phylogeny was constructed to account for relatedness. ResultsWild tomato species can be differentiated by their VOCs, withSolanum pennelliinotably distinct. Phylogenetic conservatism exists to a limited extent. Major cladewide patterns corresponded to divergence of the five brightly colored‐fruited species from the nine green‐fruited species, particularly for nitrogen‐containing compounds (higher in colored‐fruited) and esters (higher in green‐fruited), the latter appearing to signal a sugar reward. ConclusionsWe established a framework for fruit scent evolution studies in a crop wild relative system, showing that each species in the tomato clade has a unique VOC profile. Differences between color groups align with fruit syndromes that could be driven by selection from frugivores. The evolution of colored fruits was accompanied by changes in biosynthetic pathways for esters and nitrogen‐containing compounds, volatiles important to tomato flavor. 

Abstract Weedy rice (Oryzaspp.) is a weedy relative of the cultivated rice that competes with the crop and causes significant production loss. The BHA (blackhull awned) US weedy rice group has evolved fromauscultivated rice and differs from its ancestors in several important weediness traits, including flowering time, plant height and seed shattering. Prior attempts to determine the genetic basis of weediness traits in plants using linkage mapping approaches have not often considered weed origins. However, the timing of divergence between crossed parents can affect the detection of quantitative trait loci (QTL) relevant to the evolution of weediness. Here, we used a QTL‐seq approach that combines bulked segregant analysis and high‐throughput whole genome resequencing to map the three important weediness traits in an F₂population derived from a cross between BHA weedy rice with an ancestralauscultivar. We compared these QTLs with those previously detected in a cross of BHA with a more distantly related crop,indica. We identified multiple QTLs that overlapped with regions under selection during the evolution of weedy BHA rice and some candidate genes possibly underlying the evolution weediness traits in BHA. We showed that QTLs detected with ancestor–descendant crosses are more likely to be involved in the evolution of weediness traits than those detected from crosses of more diverged taxa. 

The seed shattering trait has been repeatedly reshaped during rice evolution. Reduced in cultivated rice and increased in weedy rice, shattering is of great agronomic importance because of its association with yield losses. Since its first descriptions, the phenotypic patterns and the genetic regulation of cultivated and weedy rice seed shattering have been extensively studied, with a variety of methods and techniques. The aim of this review is to discuss and recommend the most suitable experimental methods for phenotypic and molecular evaluation of seed shattering in cultivated and weedy rice. Rice seed shattering must be quantified, preferably, by breaking tensile strength (BTS) assays, because other methods are more prone to human errors. The evaluation time is particularly important, and the developmental stages of the panicles measured need to be recorded. QTL analyses and GWAS studies are suitable for discovery of genes influencing shattering, but the resulting genes may only be relevant in the parental lines or the populations used. The variety of cultivated rice and evolutionary origin of weedy rice accessions has a great influence on results of rice seed shattering phenotypic and genotypic analyses and needs to always be taken into account. 

Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including LIN5 , ALMT9 , AAT1 , CXE1 , and LoxC . The aim of this study was to identify any association of these genes with trait variation and to describe the genetic diversity at these loci in the red-fruited tomato clade comprised of the wild ancestor Solanum pimpinellifolium , the semi-domesticated species Solanum lycopersicum cerasiforme and early domesticated Solanum lycopersicum . High genetic diversity was observed at these five loci, including novel haplotypes that could be incorporated into breeding programs to improve fruit quality of modern tomatoes. Using newly available high-quality genome assemblies, we assayed each gene for potential functional causative polymorphisms and resolved a duplication at the LoxC locus found in several wild and semi-domesticated accessions which caused lower accumulation of lipid derived volatiles. In addition, we explored gene expression of the five genes in nine phylogenetically diverse tomato accessions. In general, the expression patterns of these genes increased during fruit ripening but diverged between accessions without clear relationship between expression and metabolite levels.