Ribosomal gene spacer length variability in cultivated and wild rice species

Summary Restriction fragment length polymorphism of the rDNA spacer was studied in the genus Oryza using a cloned rice rDNA probe. One-hundred-five accessions, including 58 cultivated rice and 47 wild species with various genome types, were analysed. Seven size classes differing from one another by an increment of ca. 300 bp were observed amongst the Asiatic cultivated rice of the species O. sativa. A general tendency from a smaller spacer in the Japonica subtypes to longer ones in Indica is observed. Classification as Japonica or Indica on the basis of rDNA pattern generally agrees with classification based on isozyme patterns. In contrast, African rice of the species O. glaberrima does not display any rDNA size variation. When wild species are considered, extensive variation is observed, but the fragment sizes do not fall into regularly increasing size classes except for O. rufipogon and O. longistaminata. The variation is greater in these species than in the cultivated ones.     

A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome

Most reported examples of change in vertebrate mitochondrial (mt) gene order could be explained by a tandem duplication followed by random loss of redundant genes (tandem duplication-random loss [TDRL] model). Under this model of evolution, independent loss of genes arising from a single duplication in an ancestral species are predicted, and remnant pseudogenes expected, intermediate states that may remain in rearranged genomes. However, evidence for this is rare and largely scattered across vertebrate lineages. Here, we report new derived mt gene orders in the vertebrate "WANCY" region of four closely related caecilian amphibians. The novel arrangements found in this genomic region (one of them is convergent with the derived arrangement of marsupials), presence of pseudogenes, and positions of intergenic spacers fully satisfy predictions from the TDRL model. Our results, together with comparative data for the available vertebrate complete mt genomes, provide further evidence that the WANCY genomic region is a hotspot for gene order rearrangements and support the view that TDRL is the dominant mechanism of gene order rearrangement in vertebrate mt genomes. Convergent gene rearrangements are not unlikely in hotspots of gene order rearrangement by TDRL.     

A novel functional gene associated with cold tolerance at the seedling stage in rice

Identification and cloning of cold‐tolerant genes that can stably express under different cold environments are crucial for molecular rice breeding for cold tolerance. In the previous study, we identified a cold‐tolerant QTL at the seedling stage, qCTS‐9 which could be detected under different cold environments using a recombinant inbred line (RIL) population derived from a cold‐tolerant variety Lijiangxintuanheigu (LTH) and a cold‐sensitive variety Shanhuangzhan 2 (SHZ‐2). In this study, eight candidate genes within the qCTS‐9 interval were identified through integrated analysis of QTL mapping with genomewide differential expression profiling of LTH. The qRT‐PCR assay showed that only Os09g0410300 exhibited different expression patterns between LTH and SHZ‐2 during cold stress, and significantly positive correlation was found between cold induction of Os09g0410300 and seedling cold tolerance in the RI lines. Five SNPs and one InDel in the promoters of Os09g0410300 were detected between LTH and SHZ‐2, and the InDel marker ID410300 designed based on the insertion–deletion polymorphism in the promoter was significantly associated with seedling cold tolerance in RIL population. Further, Os09g0410300 over‐expression plants exhibited enhanced cold tolerance at the seedling stage compared with the wild‐type plants. Thus, our results suggest that Os09g0410300 is the functional gene underlying qCTS‐9. To our knowledge, it is a novel gene contributed to enhance cold tolerance at the seedling stage in rice. Identification of the functional gene underlying qCTS‐9 and development of the gene‐specific marker will facilitate molecular breeding for cold tolerance at the seedling stage in rice through transgenic approach and marker‐assisted selection (MAS).     

Incipient allochronic speciation due to non-selective assortative mating by flowering time, mutation and genetic drift

We model the evolution of flowering time using a multilocus quantitative genetic model with non-selective assortative mating and mutation to investigate incipient allochronic speciation in a finite population. For quantitative characters with evolutionary parameters satisfying empirical observations and two approximate inequalities that we derived, disjunct clusters in the population flowering phenology originated within a few thousand generations in the absence of disruptive natural or sexual selection. Our simulations and the conditions we derived showed that cluster formation was promoted by limited population size, high mutational variance of flowering time, short individual flowering phenology and a long flowering season. By contrast, cluster formation was hindered by inbreeding depression, stabilizing selection and pollinator limitation. Our results suggest that incipient allochronic speciation in populations of limited size (satisfying two inequalities) could be a common phenomenon.     

Whole-genome assembly and annotation of northern wild rice,Zizania palustris L., supports a whole-genome duplication in the Zizania genus

Zizania palustris L. (northern wild rice, NWR) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural and agricultural significance, specifically in the Great Lakes region of the USA. Using flow cytometry, we first estimated the NWR genome size to be 1.8 Gb. Using long- and short-range sequencing, Hi-C scaffolding and RNA-seq data from eight tissues, we generated an annotated whole-genome de novo assembly of NWR. The assembly was 1.29 Gb in length, highly repetitive (approx. 76.0%) and contained 46 421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole-genome duplication (WGD) after the Zizania–Oryza speciation event have both led to an increase in the genome size of NWR in comparison with Oryza sativa L. and Zizania latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed the conservation of large syntenic blocks between NWR and O. sativa, which were used to identify putative seed-shattering genes. Estimates of divergence times revealed that the Zizania genus diverged from Oryza approximately 26–30 million years ago (26–30 MYA), whereas NWR and Z. latifolia diverged from one another approximately 6–8 MYA. Comparative genomics confirmed evidence of a WGD in the Zizania genus and provided support that the event occurred prior to the NWR–Z. latifolia speciation event. This genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.     

Mapping quantitative trait loci associated with days to flowering and photoperiod sensitivity in rice (Oryza sativa L.)

This study was undertaken to identify putative quantitative trait loci (QTLs) associated with days to flowering (DTF) and photoperiod response in rice. A population of 143 recombinant inbred lines derived from a cross between CO39 and Moroberekan was grown under greenhouse conditions and exposed to two different photoperiod regimes. DTF of individual plants was evaluated under 10 h and 14 h day lengths, and loci associated with photoperiod sensitivity were identified based on the delay in flowering under the 14 h photoperiod (DTF at 14 h minus DTF at 10 h). An RFLP data set consisting of 127 markers provided the basis for the QTL analysis. Both single marker and interval analysis were used and interactions between putative QTLs were estimated based on two-way ANOVA. Out of 15 QTLs associated with DTF, only 4 were identified as influencing the response to photoperiod. Interactions between flowering QTLs indicated the complex nature of the control of flowering in rice. The effectiveness of using a single recombinant inbred population to study a variety of complex phenotypes is discussed in relation to practical plant breeding.