Given the disposability of somatic tissue, selection can favor a higher mutation rate in the early segregating soma than in germline, as seen in some animals. Although in plants intra-organismic mutation rate heterogeneity is poorly resolved, the same selectionist logic can predict a lower rate in shoot than in root and in longer-lived terminal tissues (e.g., leaves) than in ontogenetically similar short-lived ones (e.g., petals), and that mutation rate heterogeneity should be deterministic with no significant differences between biological replicates. To address these expectations, we sequenced 754 genomes from various tissues of eight plant species. Consistent with a selectionist model, the rate of mutation accumulation per unit time in shoot apical meristem is lower than that in root apical tissues in perennials, in which a high proportion of mutations in shoots are themselves transmissible, but not in annuals, in which somatic mutations tend not to be transmissible. Similarly, the number of mutations accumulated in leaves is commonly lower than that within a petal of the same plant, and there is no more heterogeneity in accumulation rates between replicate branches than expected by chance. High mutation accumulation in runners of strawberry is, we argue, the exception that proves the rule, as mutation transmission patterns indicate that runner has a restricted germline. However, we also find that in vitro callus tissue has a higher mutation rate (per unit time) than the wild-grown comparator, suggesting nonadaptive mutational “fragility”. As mutational fragility does not obviously explain why the shoot—root difference varies with plant longevity, we conclude that some mutation rate variation between tissues is consistent with selectionist theory but that a mechanistic null of mutational fragility should be considered. Whereas there has been considerable attention paid to understanding differences in the mutation rate between different species, much less is known about variation in the mutation rate within individuals of multicellular species. In animals, evidence suggests that the segregated germline has a lower mutation rate than somatic cells, which accords with an adaptive model of intra-organism mutation rate variation. Here, we consider related questions in plants, which, although not having an early segregated germline, present numerous opportunities to test such an adaptive model. In particular, such a model would predict a lower rate in shoots than in roots and in relatively long-lived leaves compared with ontogenetically related but more ephemeral petals. In addition, we expect that mutation rate variation should be deterministic, such that there is no more heterogeneity in mutation rates between similarly aged branches than expected by chance. By sequencing several hundred genomes for numerous different species, we find all predictions to be supported, with the proviso that the root—shoot difference is witnessed in perennials but not in an annual. This last difference we show to be explicable, as annuals transmit relatively few premeiotic mutations. Although the adaptive model is then parsimonious, we caution that the mutation rate in plants can be easily affected by local conditions, as evidenced by large differences between lab-grown callus and field-grown plants.

Tetep is a rice cultivar known for broad-spectrum resistance to blast, a devastating fungal disease. The molecular basis for its broad-spectrum resistance is still poorly understood. Is it because Tetep has many more NLR genes than other cultivars? Or does Tetep possess multiple major NLR genes that can individually confer broad-spectrum resistance to blast? Moreover, are there many interacting NLR pairs in the Tetep genome? We sequenced its genome, obtained a high-quality assembly, and annotated 455 nucleotide-binding site leucine-rich repeat ( NLR ) genes. We cloned and tested 219 NLR genes as transgenes in 2 susceptible cultivars using 5 to 12 diversified pathogen strains; in many cases, fewer than 12 strains were successfully cultured for testing. Ninety cloned NLR s showed resistance to 1 or more pathogen strains and each strain was recognized by multiple NLR s. However, few NLR s showed resistance to >6 strains, so multiple NLR s are apparently required for Tetep’s broad-spectrum resistance to blast. This was further supported by the pedigree analyses, which suggested a correlation between resistance and the number of Tetep-derived NLR s. In developing a method to identify NLR pairs each of which functions as a unit, we found that >20% of the NLR s in the Tetep and 3 other rice genomes are paired. Finally, we designed an extensive set of molecular markers for rapidly introducing clustered and paired NLR s in the Tetep genome for breeding new resistant cultivars. This study increased our understanding of the genetic basis of broad-spectrum blast resistance in rice.

Mutation rates vary between species, between strains within species and between regions within a genome. What are the determinants of these forms of variation? Here, via parent–offspring sequencing of the peach we ask whether (i) woody perennials tend to have lower per unit time mutation rates compared to annuals, and (ii) hybrid strains have high mutation rates. Between a leaf from a low heterozygosity individual, derived from an intraspecific cross, to a leaf of its selfed progeny, the mutation rate is 7.77 × 10⁻⁹point mutations per bp per generation, similar toArabidopsis thaliana(7.0–7.4 × 10⁻⁹point mutations per bp per generation). This suggests a low per unit time mutation rate as the generation time is much longer in peach. This is supported by our estimate of 9.48 × 10⁻⁹point mutations per bp per generation from a 200-year-old low heterozygosity peach to its progeny. From a more highly heterozygous individual derived from an interspecific cross to its selfed progeny, the mutation rate is 1.38 × 10⁻⁸mutations per site per generation, consistent with raised rates in hybrids. Our data thus suggest that (i) peach has an approximately order of magnitude lower mutation rate per unit time thanArabidopsis, consistent with reports of low evolutionary rates in woody perennials, and (ii) hybridization may, indeed, be associated with increased mutation rates as considered over a century ago.

Repeated artificial selection of a complex trait facilitates the identification of genes underlying the trait, especially if multiple selected descendant lines are available. Here we developed a pedigree-based approach to identify genes underlying the Green Revolution (GR) phenotype. From a pedigree analysis, we selected 30 cultivars including the “miracle rice” IR8, a GR landmark, its ancestors and descendants, and also other related cultivars for identifying high-yield genes. Through sequencing of these genomes, we identified 28 ancestral chromosomal blocks that were maintained in all the high-yield cultivars under study. In these blocks, we identified six genes of known function, including the GR gene sd1, and 123 loci with genes of unknown function. We randomly selected 57 genes from the 123 loci for knockout or knockdown studies and found that a high proportion of these genes are essential or have phenotypic effects related to rice production. Notably, knockout lines have significant changes in plant height (P < 0.003), a key GR trait, compared with wild-type lines. Some gene knockouts or knockdowns were especially interesting. For example, knockout of Os10g0555100, a putative glucosyltransferase gene, showed both reduced growth and altered panicle architecture. In addition, we found that in some retained chromosome blocks several GR-related genes were clustered, although they have unrelated sequences, suggesting clustering of genes with similar functions. In conclusion, we have identified many high-yield genes in rice. Our method provides a powerful means to identify genes associated with a specific trait. Significance Finding the genes that control a complex trait is difficult because each gene may have only minor phenotypic effects. Quantitative trait loci mapping and genome-wide association study techniques have been developed for this purpose but are laborious and time-consuming. Here we developed a method combining pedigree analysis, whole-genome sequencing, and CRISPR-Cas9 technology. By sequencing the parents and descendants of IR8, the Green Revolution “miracle rice,” we identified many genes that had been retained in the pedigree by selection for high yield. Knockout and knockdown studies showed that a large proportion of the identified genes are essential or have phenotypic effects related to production. Our approach provides a powerful means for identifying genes involved in a complex trait.