A transposon-derived gene family regulates heading date in rice.

As a consequence of transposon domestication, transposon-derived proteins often acquire important biological functions. However, there have been limited studies on transposon-derived proteins in rice, and a systematic analysis of transposon-derived genes is lacking. Here, for the first time, we conducted a comprehensive analysis of the DDE_Tnp_4 (DDE) gene family, which originated from transposons but lost their transpositional ability and acquired new gene functions in Oryza species. A total of 58 DDE family genes, categorized into six groups, were identified in Oryza species, including 13 OsDDE genes in Oryza sativa ssp. japonica. Our analysis indicates that gene duplication events were not the primary mechanism behind the expansion of OsDDE genes in rice. Promoter cis-element analysis combined with haplotype analysis confirmed that OsDDEs regulate the heading date in rice. Specifically, OsDDE9 is a nuclear-localized protein expressed ubiquitously, which promotes heading date by regulating the expression of Ghd7 and Ehd1 under both short-day and long-day conditions. Single-nucleotide polymorphism (SNP) variations in the OsDDE9 promoter leads to changes in promoter activity, resulting in variations in heading dates. This study provides valuable insights into the molecular function and mechanism of the OsDDE genes.

Variation in Rice Plastid Genomes in Wide Crossing Reveals Dynamic Nucleo-Cytoplasmic Interaction.

Plastid genomes (plastomes) of angiosperms are well known for their relative stability in size, structure, and gene content. However, little is known about their heredity and variations in wide crossing. To such an end, the plastomes of five representative rice backcross inbred lines (BILs) developed from crosses of O. glaberrima/O. sativa were analyzed. We found that the size of all plastomes was about 134,580 bp, with a quadripartite structure that included a pair of inverted repeat (IR) regions, a small single-copy (SSC) region and a large single-copy (LSC) region. They contained 76 protein genes, 4 rRNA genes, and 30 tRNA genes. Although their size, structure, and gene content were stable, repeat-mediated recombination, gene expression, and RNA editing were extensively changed between the maternal line and the BILs. These novel discoveries demonstrate that wide crossing causes not only nuclear genomic recombination, but also plastome variation in plants, and that the plastome plays a critical role in coordinating the nuclear-cytoplasmic interaction.

Creation of Elite Rice with High-Yield, Superior-Quality and High Resistance to Brown Planthopper Based on Molecular Design.

Breeding rice (Oryza sativa L.) with high yield, superior quality, desired grain shape and high resistance is the goal of breeding to meet the needs of current consumers. It is usually hard to combine multiple complex traits based on traditional breeding methods because they are frequently antagonistic to each other. However, molecular design breeding, as a novel breeding method, is an optional alternative to this challenge. To demonstrate molecular design breeding, 15 favorable genes from five parent lines were pyramided together to develop elite rice with high-yield, superior-quality, desired grain shape and high resistance to brown planthopper (BPH). The parental lines were 9311, the recurrent parent, carrying APO1, Ghd7, Ghd8 and Gn1a for high yield, GS3 and qSW5 for grain shape, and Wx and ALK for eating and cooking quality; 1880 with Gn8.1 for large panicles; Luo-Yu-Xiang carrying GW7 for grain shape and SBE3, SSIV2 and SSIII for eating and cooking quality; Luoyang6 with Bph6 and Luoyang9 with Bph9 for BPH resistance. After careful screening for the 15 targeted genes, desired phenotype and maximum genetic background from 9311, three molecular design lines with desired phenotypes, named as MD1 (Molecular design 1), MD2 and MD3 were developed. MD3 carried all 15 targeted genes, and MD1 and MD2 had 14 of the 15 targeted genes. Only SBE3 was not introgressed into MD1 and MD2 but this had minimal impact on the gel consistency and alkali spreading value. These newly bred lines exhibited higher yield potential, better grain quality with slender grains, low amylose content, high gel consistency and alkali spreading value, and higher BPH resistance compared to the parent 9311. In this study, we successfully created three novel rice lines with high yield, superior quality and improved BPH resistance by rational molecular design. Our results demonstrate molecular design is a powerful strategy to improve multiple complex traits and will provide a reference for the future commercial rice improvement.

Quantitative Trait Loci Mapping of Mineral Element Contents in Brown Rice Using Backcross Inbred Lines Derived From Oryza longistaminata.

Mineral elements play an extremely important role in human health, and are worthy of study in rice grain. Wild rice is an important gene pool for rice improvement including grain yield, disease, and pest resistance as well as mineral elements. In this study, we identified 33 quantitative trait loci (QTL) for Fe, Zn, Se, Cd, Hg, and As contents in wild rice Oryza longistaminata. Of which, 29 QTLs were the first report, and 12 QTLs were overlapped to form five clusters as qSe1/qCd1 on chromosome 1, qCd4.2/qHg4 on chromosome 4, qFe5.2/qZn5.2 on chromosome 5, qFe9/qHg9.2/qAs9.2 on chromosome 9, and qCd10/qHg10 on chromosome 10. Importantly, qSe1/qCd1, can significantly improve the Se content while reduce the Cd content, and qFe5.2/qZn5.2 can significantly improve both the Fe and Zn contents, they were delimited to an interval about 53.8 Kb and 26.2 Kb, respectively. These QTLs detected from Oryza longistaminata not only establish the basis for subsequent gene cloning to decipher the genetic mechanism of mineral element accumulation, but also provide new genetic resource for rice quality improvement.

Deciphering the Genetic Basis of Lodging Resistance in Wild Rice Oryza longistaminata.

The abuse of fertilizer results in tall rice plants that are susceptible to lodging and reduced plant yield. Hence, it is important to identify and utilize the quantitative trait loci (QTLs)/genes for lodging resistance breeding. Oryza longistaminata exhibits a strong stem and high biomass productivity, which could be a candidate gene pool for cultivars lodging resistance improvement. Here, a set of 152 BC2F20 lines derived from a cross between a cultivated line 93-11 and O. longistaminata was evaluated for lodging resistance. QTL mapping analysis combined with single-nucleotide polymorphism (SNP) marker derived from high-throughput sequencing identified 12 QTLs for stem diameter (SD), 11 QTLs for stem length (SL), and 3 QTLs for breaking strength (BS). Of which, 14 QTLs were first identified from O. longistaminata. A major QTL, qLR1, which was delimited to a region ∼80 kb on chromosome 1, increased stem diameter, stem length, and breaking strength. Another major QTL, qLR8, that was delimited in an interval ∼120 kb on chromosome 8, significantly enhanced the breaking strength. These results provide evidence that O. longistaminata can be exploited to develop lodging-resistant rice lines.

Wide crossing diversify mitogenomes of rice.

BACKGROUND: In most angiosperms, the inheritance of the mitochondria takes place in a typical maternal manner. However, very less information is available about if the existence of structural variations or not in mitochondrial genomes (mitogenomes) between maternal parents and their progenies. RESULTS: In order to find the answer, a stable rice backcross inbred line (BIL) population was derived from the crosses of Oryza glaberrima/Oryza sativa//Oryza sativa. The current study presents a comparative analysis of the mitogenomes between maternal parents and five BILs. There were recorded universal structural variations such as reversal, translocation, fusion, and fission among the BILs. The repeat-mediated recombination and non-homologous end-joining contributed virtually equal to the rearrangement of mitogenomes. Similarly, the relative order, copy-number, expression level, and RNA-editing rate of mitochondrial genes were also extensively varied among BILs. CONCLUSIONS: These novel findings unraveled an unusual mystery of the maternal inheritance and possible cause for heterogeneity of mitogenomes in rice population. The current piece of work will greatly develop our understanding of the plant nucleo-cytoplasmic interaction and their potential role in plant growth and developmental processes.

Quantitative Trait Locus Mapping of the Combining Ability for Yield-Related Traits in Wild Rice Oryza longistaminata.

In decades of hybrid rice breeding, the combining ability has been successfully used to evaluate excellent parental lines and predict heterosis. However, previous studies for the combining ability mainly focused on cultivated rice and rarely involved wild rice. In this study, for the first time, we identified 20 new quantitative trait loci (QTLs) for the combining ability in wild rice using a North Carolina II mating design. Among them, qGCA1, one of the major QTLs that can significantly improve the general combining ability of the plant height, spikelet number, and yield per plant, was delimited to an interval of about 72 kb on chromosome 1. qSCA8, another major QTL, which can significantly improve the specific combining ability of the seed-setting rate and yield per plant, was located in an interval of about 90 kb on chromosome 8. These QTLs discovered from wild rice will provide new ideas to explain the genetic mechanism of the combining ability and establish the basis for breeding of high-combining-ability rice.

QTL Mapping of Seed Vigor of Backcross Inbred Lines Derived From Oryza longistaminata Under Artificial Aging.

Seed vigor is an important character of seed quality that promotes rice to germinate rapidly from soil and developing to a strong seedling, especially in the current rice direct-sowing production system. However, previous studies for seed vigor mainly concentrate in cultivars, and less reports involving in wild rice. In this study, 152 backcross inbred lines (BILs) derived from wild rice Oryza longistaminata were genotyped with re-sequencing technology, and QTLs for seed vigor related traits under normal and artificial aging treatment were analyzed. Totally, 36 QTLs were detected, of which, eight for germination potential (GP), 10 for germination rate (GR), 9 for seedling length (SL), and 9 for root length (RL). Among these, 14 novel QTLs were identified from O. longistaminata. Of which, six QTLs were related to germination, and eight related to seedling growth under aging stress. What's more, the major QTLs q9SL1.1, q6SL1.1, and q3SL1.1 for seedling length were fallen in the same locus and fine-mapped an interval about 90 Kb. The major QTLs q9GR8.1 and q9GP8.1 related with germination were fine-mapped to an interval about 90 Kb. This work will provide us basis for breeding of high seed vigor rice in rice breeding programs and further cloning of these genes.

Development of Elite BPH-Resistant Wide-Spectrum Restorer Lines for Three and Two Line Hybrid Rice.

Hybrid rice has contributed significantly to the world food security. Breeding of elite high-yield, strong-resistant broad-spectrum restorer line is an important strategy for hybrid rice in commercial breeding programs. Here, we developed three elite brown planthopper (BPH)-resistant wide-spectrum restorer lines by pyramiding big-panicle gene Gn8.1, BPH-resistant genes Bph6 and Bph9, fertility restorer genes Rf3, Rf4, Rf5, and Rf6 through molecular marker assisted selection. Resistance analysis revealed that the newly developed restorer lines showed stronger BPH-resistance than any of the single-gene donor parent Luoyang-6 and Luoyang-9. Moreover, the three new restorer lines had broad spectrum recovery capabilities for Honglian CMS, Wild abortive CMS and two-line GMS sterile lines, and higher grain yields than that of the recurrent parent 9,311 under nature field conditions. Importantly, the hybrid crosses also showed good performance for grain yield and BPH-resistance. Thus, the development of elite BPH-resistant wide-spectrum restorer lines has a promising future for breeding of broad spectrum BPH-resistant high-yield varieties.

Artificial Selection of Gn1a Plays an Important role in Improving Rice Yields Across Different Ecological Regions.

BACKGROUND: Rice is one of the most important crops, and it is essential to improve rice productivity to satisfy the future global food supply demands. Gn1a (OsCKX2), which encodes cytokinin oxidase/dehydrogenase, plays an important role in regulating rice grain yield. RESULTS: In this study, we analyzed the genetic variation of Gn1a, which influences grain yield through controlling the number of spikelets in rice. The allelic variations in the promoter, 5' untranslated region (UTR) and coding sequence (CDS) of Gn1a were investigated in 175 cultivars and 21 wild rice accessions. We found that Gn1a showed less sequence variation in the cultivars, but exhibited significant nucleotide diversity in wild rice. A total of 14 alleles, named AP1 to AP14, were identified in the cultivars based on the amino acid divergence of GN1A. Association analysis revealed that the number of spikelets and grain yield were significantly different between the different alleles. Phylogenetic analysis indicated that the three main alleles, AP3, AP8 and AP9, in the cultivars might originate from a common ancestor allele, AP1, in wild rice. CONCLUSIONS: Of these alleles in the cultivars, AP9 was suggested as the best allele in indica, as it has shown strong artificial selection in breeding high-yield rice in the past. It might be valuable to explore the high-yield-related alleles of Gn1a to develop high-yield rice cultivars in future breeding programs.