Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster.

We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plant height in CR4379, a near-isogenic line from a cross between Oryza sativa spp. japonica cultivar 'Hwaseong' and the wild relative Oryza rufipogon. Map-based cloning and transgenic approaches revealed that APX9, which encodes an l-ascorbate peroxidase 4, is associated with this cluster. A 3 bp InDel was observed leading to the addition of a valine in Hwaseong compared with O. rufipogon. APX9-overexpressing transgenic plants in the Hwaseong background were taller than Hwaseong. Consistent with these results, APX9 T-DNA insertion mutants in the japonica cultivar Dongjin were shorter. These results confirm that APX9 is the causal gene for the QTL cluster. Sequence analysis of APX9 from 303 rice accessions revealed that the 3 bp InDel clearly differentiates japonica (APX9HS) and O. rufipogon (APX9OR) alleles. indica accessions shared both alleles, suggesting that APX9HS was introgressed into indica followed by crossing. The finding that O. rufipogon accessions with different origins carry APX9OR suggests that the 3 bp insertion was specifically selected in japonica during its domestication. Our findings demonstrate that APX9 acts as a major regulator of plant development by controlling a valuable suite of agronomically important traits in rice.

A RING-Type E3 Ubiquitin Ligase, OsGW2, Controls Chlorophyll Content and Dark-Induced Senescence in Rice.

Leaf senescence is the final stage of plant development. Many internal and external factors affect the senescence process in rice (Oryza sativa L.). In this study, we identified qCC2, a major quantitative trait locus (QTL) for chlorophyll content using a population derived from an interspecific cross between O. sativa (cv. Hwaseong) and Oryza grandiglumis. The O. grandiglumis allele at qCC2 increased chlorophyll content and delayed senescence. GW2 encoding E3 ubiquitin ligase in the qCC2 region was selected as a candidate for qCC2. To determine if GW2 is allelic to qCC2, a gw2-knockout mutant (gw2-ko) was examined using a dark-induced senescence assay. gw2-ko showed delayed leaf senescence in the dark with down-regulated expression of senescence-associated genes (SAGs) and chlorophyll degradation genes (CDGs). The association of the GW2 genotype with the delayed senescence phenotype was confirmed in an F2 population. RNA-seq analysis was conducted to investigate 30-day-old leaf transcriptome dynamics in Hwaseong and a backcross inbred line-CR2002-under dark treatment. This resulted in the identification of genes involved in phytohormone signaling and associated with senescence. These results suggested that transcriptional regulation was associated with delayed senescence in CR2002, and RING-type E3 ubiquitin ligase GW2 was a positive regulator of leaf senescence in rice.

Sequencing and Comparative Analysis of the Chloroplast Genome of Angelica polymorpha and the Development of a Novel Indel Marker for Species Identification.

The genus Angelica (Apiaceae) comprises valuable herbal medicines. In this study, we determined the complete chloroplast (CP) genome sequence of A. polymorpha and compared it with that of Ligusticum officinale (GenBank accession no. NC039760). The CP genomes of A. polymorpha and L. officinale were 148,430 and 147,127 bp in length, respectively, with 37.6% GC content. Both CP genomes harbored 113 unique functional genes, including 79 protein-coding, four rRNA, and 30 tRNA genes. Comparative analysis of the two CP genomes revealed conserved genome structure, gene content, and gene order. However, highly variable regions, sufficient to distinguish between A. polymorpha and L. officinale, were identified in hypothetical chloroplast open reading frame1 (ycf1) and ycf2 genic regions. Nucleotide diversity (Pi) analysis indicated that ycf4⁻chloroplast envelope membrane protein (cemA) intergenic region was highly variable between the two species. Phylogenetic analysis revealed that A. polymorpha and L. officinale were well clustered at family Apiaceae. The ycf4-cemA intergenic region in A. polymorpha carried a 418 bp deletion compared with L. officinale. This region was used for the development of a novel indel marker, LYCE, which successfully discriminated between A. polymorpha and L. officinale accessions. Our results provide important taxonomic and phylogenetic information on herbal medicines and facilitate their authentication using the indel marker.

Comprehensive identification of LMW-GS genes and their protein products in a common wheat variety.

Although it is well known that low-molecular-weight glutenin subunits (LMW-GS) from wheat affect bread and noodle processing quality, the function of specific LMW-GS proteins remains unclear. It is important to find the genes that correspond to individual LMW-GS proteins in order to understand the functions of specific proteins. The objective of this study was to link LMW-GS genes and haplotypes characterized using well known Glu-A3, Glu-B3, and Glu-D3 gene-specific primers to their protein products in a single wheat variety. A total of 36 LMW-GS genes and pseudogenes were amplified from the Korean cultivar Keumkang. These include 11 Glu-3 gene haplotypes, two from the Glu-A3 locus, two from the Glu-B3 locus, and seven from the Glu-D3 locus. To establish relationships between gene haplotypes and their protein products, a glutenin protein fraction was separated by two-dimensional gel electrophoresis (2-DGE) and 17 protein spots were analyzed by N-terminal amino acid sequencing and tandem mass spectrometry (MS/MS). LMW-GS proteins were identified that corresponded to all Glu-3 gene haplotypes except the pseudogenes. This is the first report of the comprehensive characterization of LMW-GS genes and their corresponding proteins in a single wheat cultivar. Our approach will be useful to understand the contributions of individual LMW-GS to the end-use quality of flour.

Rice PCR1 influences grain weight and Zn accumulation in grains.

Proteins containing a placenta-specific 8 domain (PLAC8) function as major organ size regulators in Solanum lycopersicum and Zea may, and putative metal ion transporters in Arabidopsis thaliana, Oryza sativa and Brassica juncea. However, it is unknown how PLAC8 domain-containing proteins fulfill such diverse roles. Here, we found that plant cadmium resistance 1 (PCR1) influences both zinc (Zn) accumulation and grain weight in rice. OsPCR1 knockout and knockdown lines produced lighter grains than the wild type, while OsPCR1 overexpression lines produced heavier grains. Furthermore, the grains of OsPCR1 knockdown lines exhibited substantially higher Zn and lower cadmium (Cd) concentrations than the control, as did yeast heterologously expressing OsPCR1. Through sequence analysis, we showed that the amino acid sequence of japonica-type PCR1 was distinct from that of indica-type and wild rice accessions. This difference was correlated with distinct Zn-related phenotypes. Japonica-type PCR1 had a shorter N-terminus than did PCR1 in the other rice types, and yeast heterologously expressing japonica-type PCR1 was more sensitive to Zn than was yeast expressing indica-type PCR1. Furthermore, japonica-type grains accumulated less Zn than did indica-type grains. Our study suggests that rice PCR1 maintains metal ion homeostasis and grain weight and might have been selected for during domestication.

Phytochelatin-metal(loid) transport into vacuoles shows different substrate preferences in barley and Arabidopsis.

Cadmium (Cd) and arsenic (As) are toxic to all living organisms, including plants and humans. In plants, Cd and As are detoxified by phytochelatins (PCs) and metal(loid)-chelating peptides and by sequestering PC-metal(loid) complexes in vacuoles. Consistent differences have been observed between As and Cd detoxification. Whereas chelation of Cd by PCs is largely sufficient to detoxify Cd, As-PC complexes must be sequestered into vacuoles to be fully detoxified. It is not clear whether this difference in detoxification pathways is ubiquitous among plants or varies across species. Here, we have conducted a PC transport study using vacuoles isolated from Arabidopsis and barley. Arabidopsis vacuoles accumulated low levels of PC2 -Cd, and vesicles from yeast cells expressing either AtABCC1 or AtABCC2 exhibited negligible PC2 -Cd transport activity compared with PC2 -As. In contrast, barley vacuoles readily accumulated comparable levels of PC2 -Cd and PC2 -As. PC transport in barley vacuoles was inhibited by vanadate, but not by ammonium, suggesting the involvement of ABC-type transporters. Interestingly, barley vacuoles exhibited enhanced PC2 transport activity when essential metal ions, such as Zn(II), Cu(II) and Mn(II), were added to the transport assay, suggesting that PCs might contribute to the homeostasis of essential metals and detoxification of non-essential toxic metal(loid)s.

T-DNA insertion mutants of Arabidopsis DA1 orthologous genes displayed altered plant height and yield-related traits in rice (O. Sativa L.).

BACKGROUND: The Arabidopsis DA1 gene is a key player in the regulation of organ and seed development. To extend our understanding of its functional counterparts in rice, this study investigates the roles of orthologous genes, namely DA1, HDR3, HDR3.1, and the DA2 ortholog GW2, through the analysis of T-DNA insertion mutants. OBJECTIVE: The aim of this research is to elucidate the impact of T-DNA insertions in DA1, HDR3, HDR3.1, and GW2 on agronomic traits in rice. By evaluating homozygous plants, we specifically focus on key parameters such as plant height, tiller number, days to heading, and grain size. METHODS: T-DNA insertion locations were validated using PCR, and subsequent analyses were conducted on homozygous plants. Agronomic traits, including plant height, tiller number, days to heading, and grain size, were assessed. Additionally, leaf senescence assays were performed under dark incubation conditions to gauge the impact of T-DNA insertions on this physiological aspect. RESULTS: The study revealed distinctive phenotypic outcomes associated with T-DNA insertions in HDR3, HDR3.1, GW2, and DA1. Specifically, HDR3 and HDR3.1 mutants exhibited significantly reduced plant height and smaller grain size, while GW2 and DA1 mutants displayed a notable increase in both plant height and grain size compared to the wild type variety Dongjin. Leaf senescence assays further indicated delayed leaf senescence in hdr3.1 mutants, contrasting with slightly earlier leaf senescence observed in hdr3 mutants under dark incubation. CONCLUSIONS: The findings underscore the pivotal roles of DA1 orthologous genes in rice, shedding light on their significance in regulating plant growth and development. The observed phenotypic variations highlight the potential of these genes as targets for crop improvement strategies, offering insights that could contribute to the enhancement of agronomic traits in rice and potentially other crops.

A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice.

Chlorophyll biosynthesis is a crucial biological process in plants, and chlorophyll content is one of the most important traits in rice breeding programs. In this study, we identified a lethal, chlorophyll-deficient, yellow seedling (YS) phenotype segregating in progeny of CR5055-21, an F2 plant derived from a backcross between Korean japonica variety 'Hwaseong' (Oryza sativa) and CR5029, which is mostly Hwaseong with a small amount of Oryza grandiglumis chromosome segments. The segregation of the mutant phenotype was consistent with a single gene recessive mutation. Light microscopy of YS leaf cross-sections revealed loosely arranged mesophyll cells and sparse parenchyma in contrast to wildtype. In addition, transmission electron microscopy showed that chloroplasts did not develop in the mesophyll cells of the YS mutant. Quantitative trait loci (QTL)-seq analysis did not detect any significant QTL, however, examination of the individual delta-SNP index identified a 2-bp deletion (AG) in the OsCHLI gene, a magnesium (Mg)-chelatase subunit. A dCAPs marker was designed and genotyping of a segregating population (n = 275) showed that the mutant phenotype co-segregated with the marker. The 2-bp deletion was predicted to result in a frameshift mutation generating a premature termination. The truncated protein likely affects formation and function of Mg-chelatase, which consists of three different subunits that together catalyze the first committed step of chlorophyll biosynthesis. Transcriptome analysis showed that photosynthesis and carbohydrate metabolism pathways were significantly altered although expression of OsCHLI was not. Chlorophyll- and carotenoid-related genes were also differentially expressed in the YS mutant. Our findings demonstrated that OsCHLI plays an important role in leaf pigment biosynthesis and leaf structure development in rice.

Brassinosteroid biosynthesis gene OsD2 is associated with low-temperature germinability in rice.

In rice, low-temperature germinability (LTG) is essential for stable stand establishment using the direct seeding method in temperate and high-altitude areas. Previously, we reported that the quantitative trait locus qLTG1 is associated with LTG. qLTG1 is also associated with tolerance to several abiotic stresses, such as salt and osmotic conditions. In this study, map-based cloning and sequence analysis indicated that qLTG1 is allelic to DWARF2 (OsD2), which encodes cytochrome P450 D2 (LOC_Os01g10040) involved in brassinosteroid (BR) biosynthesis. Sequence comparison of the two parental lines, Hwaseong and Oryza rufipogon (IRGC 105491), revealed five single nucleotide polymorphisms (SNPs) in the coding region. Three of these SNPs led to missense mutations in OsD2, whereas the other two SNPs were synonymous. We evaluated two T-DNA insertion mutants, viz., overexpression (OsD2-OE) and knockdown (OsD2-KD) mutants of OsD2, with the Dongjin genetic background. OsD2-KD plants showed a decrease in LTG and grain size. In contrast, OsD2-OE plants showed an increase in grain size and LTG. We also examined the expression levels of several BR signaling and biosynthetic genes using the T-DNA insertion mutants. Gene expression analysis and BR application experiments demonstrated that BR enhanced the seed germination rate under low-temperature conditions. These results suggest that OsD2 is associated with the regulation of LTG and improving grain size. Thus, OsD2 may be a suitable target for rice breeding programs to improve rice yield and LTG.

Characterization of Domestication Loci Associated with Awn Development in Rice.

Rice (Oryza sativa L.) is a widely studied domesticated model plant. Seed awning is an unfavorable trait during rice harvesting and processing. Hence, loss of awn was one of the target characters selected during domestication. However, the genetic mechanisms underlying awn development in rice are not well understood. In this study, we analyzed and characterized the genes for awn development using a mapping population derived from a cross between the Korean indica cultivar 'Milyang23' and a near-isogenic line NIL4/9 derived from a cross between 'Hwaseong' and Oryza minuta. Two quantitative trait loci (QTLs), qAwn4 and qAwn9, mapped on chromosomes 4 and 9, respectively, increased awn length in an additive manner. Through comparative sequencing analyses of the parental lines, LABA1 was determined as the causal gene underlying qAwn4. qAwn9 was mapped to a 199-kb physical region between markers RM24663 and RM24679. Within this interval, 27 annotated genes were identified, and five genes, including a basic leucine zipper transcription factor 76 (OsbZIP76), were considered as candidate genes for qAwn9 based on their functional annotations and sequence variations. Haplotype analysis using the candidate gene revealed tropical-japonica specific sequence variants in the qAwn9 region, which partly explains the non-detection of qAwn9 in previous studies that used progenies from interspecific crosses. This provides further evidence that OsbZIP76 is possibly a causal gene for qAwn9. The O. minuta qAwn9 allele was identified as a major QTL, providing an important molecular target for understanding the genetic control of awn development in rice. Our results lay the foundation for further cloning of the awn gene underlying qAwn9.

Interaction of starch branching enzyme 3 and granule-bound starch synthase 1 alleles increases amylose content and alters physico-chemical properties in japonica rice (Oryza sativa L.).

Four near-isogenic lines (NILs) with different allele combinations of the starch branching enzyme 3 (SBE3) and granule-bound starch synthase 1 (GBSS1) were developed by crossing the japonica rice cultivars "Dodamssal" and "Hwayeong." The associations between sequence variations in SBE3 and GBSS1, and starch-related traits were investigated. These sequence variations led to changes in seed morphology, starch structure, starch crystallinity, amylopectin chain length distribution, digestibility, apparent amylose content (AAC), and resistant starch content (RS). SBE3 and GBSS1 showed genetic interaction in regulating AAC and RS. Gene expression profiling of panicle tissues revealed significant differences in expression levels of GBSS1, SBE3, and other starch-related genes among the four NILs, indicating that variations in GBSS1 and SBE3 changed the expression level of starch-related genes. These variations contributed to the changes observed in AAC, RS, and physico-chemical characteristics of the rice starch from the NILs.

Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam.

Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation-an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.

A Novel Embryo Phenotype Associated With Interspecific Hybrid Weakness in Rice Is Controlled by the MADS-Domain Transcription Factor OsMADS8.

A novel hybrid weakness gene, DTE9, associated with a dark tip embryo (DTE) trait, was observed in CR6078, an introgression line derived from a cross between the Oryza sativa spp. japonica "Hwayeong" (HY) and the wild relative Oryza rufipogon. CR6078 seeds exhibit protruding embryos and flowers have altered inner floral organs. DTE9 was also associated with several hybrid weakness symptoms including decreased grain weight. Map-based cloning and transgenic approaches revealed that DTE9 is an allele of OsMADS8, a MADS-domain transcription factor. Genetic analysis indicated that two recessive complementary genes were responsible for the expression of the DTE trait. No sequence differences were observed between the two parental lines in the OsMADS8 coding region; however, numerous single nucleotide polymorphisms were detected in the promoter and intronic regions. We generated overexpression (OX) and RNA interference (RNAi) transgenic lines of OsMADS8 in HY and CR6078, respectively. The OsMADS8-OX lines showed the dark tip embryo phenotype, whereas OsMADS8-RNAi recovered the normal embryo phenotype. Changes in gene expression, including of ABCDE floral homeotic genes, were observed in the OsMADS8-OX and OsMADS8-RNAi lines. Overexpression of OsMADS8 led to decreased expression of OsEMF2b and ABA signaling-related genes including OsVP1/ABI3. HY seeds showed higher ABA content than CR6078 seeds, consistent with OsMADS8/DTE9 regulating the expression of genes related ABA catabolism in CR6078. Our results suggest that OsMADS8 is critical for floral organ determination and seed germination and that these effects are the result of regulation of the expression of OsEMF2b and its role in ABA signaling and catabolism.

Characterization of Quantitative Trait Loci for Germination and Coleoptile Length under Low-Temperature Condition Using Introgression Lines Derived from an Interspecific Cross in Rice.

Previously, five putative quantitative trait loci (QTLs) for low-temperature germination (LTG) have been detected using 96 BC3F8 lines derived from an interspecific cross between the Korean japonica cultivar "Hwaseong" and Oryza rufipogon. In the present study, two introgression lines, CR1517 and CR1518, were used as parents to detect additional QTLs and analyze interactions among QTLs for LTG. The F2 population (154 plants) along with parental lines, Hwaseong and O. rufipogon, were evaluated for LTG and coleoptile length under low-temperature conditions (13 °C). Among five QTLs for LTG, two major QTLs, qLTG1 and qLTG3, were consistently detected at 6 and 7 days after incubation. Three minor QTLs were detected on chromosomes 8 and 10. Two QTLs, qLTG10.1 and qLTG10.2, showing linkage on chromosome 10, exerted opposite effects with the Hwaseong allele at qLTG10.2 and the O. rufipogon allele at qLTG10.1 respectively, in turn, increasing LTG. Interactions among QTLs were not significant, implying that the QTLs act in an additive manner. Near-isogenic line plants with the combination of favorable alleles from O. rufipogon and Hwaseong exhibited higher LTG than two introgression lines. With regard to coleoptile length, three QTLs observed on chromosomes 1, 3, and 8 were colocalized with QTLs for LTG, suggesting the pleiotropy of the single gene at each locus. According to the results, the introgression of favorable O. rufipogon alleles could hasten the development of rice with high LTG and high coleoptile elongation in japonica cultivars.

Characterization of a New qLTG3-1 Allele for Low-temperature Germinability in Rice from the Wild Species Oryza rufipogon.

BACKGROUND: Rice (Oryza sativa L.) is generally sensitive to low temperatures, and in production systems that use direct-seeding, low-temperature germinability (LTG) is a desired trait. Previously, the QTLs, qLTG1 and qLTG3, that control LTG, were mapped using the BC4F8 population, which is a cross of Korean elite cultivar Hwaseong and O. rufipogon (IRGC 105491). We have characterized and analyzed the interaction between the two QTLs, by crossing TR20 that has O. rufipogon alleles at qLTG1 and qLTG3 in a Hwaseong background, with Hwaseong, to develop an F2 population. RESULTS: The F2 plants with both qLTG1 and qLTG3 alleles from O. rufipogon showed higher LTG scores, than the plants with only qLTG1 or qLTG3. No significant interaction between the qLTG1 and qLTG3 was observed, indicating that they may regulate LTG via different pathways. Based on its location, qLTG3 appears to be allelic with qLTG3-1, a major QTL known to control LTG. To investigate the genetic differences between the two parents, that were controlling LTG, we compared their qLTG3-1 sequences. In the coding region, three sequence variations leading to amino acid changes were identified between the Hwaseong and O. rufipogon. Of these, a non-synonymous substitution at the 62nd amino acid site, had not previously been reported. To understand the cause of the LTG variations between the parents, we genotyped three sequence variations of qLTG3-1, that were identified in 98 Asian cultivated rice accessions (Oryza sativa L.). The 98 accessions were classified into 5 haplotypes, based on three variations and a 71-bp deletion. Mean low-temperature germination rates were compared among the haplotypes, and haplotype 5 (O. rufipogon-type) showed a significantly higher germination rate than haplotype 2 (Nipponbare-type), and haplotype 3 (Italica Livorno-type). CONCLUSIONS: The O. rufipogon qLTG3-1 allele can be utilized for the improvement of LTG in rice breeding programs. Nearly isogenic lines harboring both qLTG1 and qLTG3-1 alleles from O. rufipogon, showed higher LTG scores than the NILs with qLTG1 or qLTG3-1 alone, and the two QTLs regulate LTG via different pathways. To our knowledge, this is the first report to detect a new qLTG3-1 allele and analyze the interaction of the two LTG QTLs in a nearly isogenic background.

Corrigendum: A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds.

[This corrects the article DOI: 10.3389/fpls.2020.564824.].

A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds.

Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica, which result from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors, and suggests that a pre-breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries (n = 63 to 81 lines per library) in both Indica (cv. IR64) and Japonica (cv. Cybonnet) backgrounds using three bio-geographically diverse wild donors representing the Oryza rufipogon Species Complex from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K rice SNP array (C7AIR) and analyzed under greenhouse conditions for several simply inherited (Mendelian) traits. These six interspecific populations can be used as individual Chromosome Segment Substitution Line libraries and, when considered together, serve as a powerful genetic resource for systematic genetic dissection of agronomic, physiological and developmental traits in rice.

Fine mapping and candidate gene analysis of the quantitative trait locus gw8.1 associated with grain length in rice.

A quantitative trait locus (QTL) gw8.1 was detected in the population derived from a cross between the elite japonica cultivar, 'Hwaseong' and Oryza rufipogon (IRGC 105491). Near isogenic lines (NILs) harboring the O. rufipogon segment on chromosome 8 showed increased grain length and weight compared to those of the recurrent parent, Hwaseong. This QTL was mapped to a 175.3-kb region containing 28 genes, of which four were considered as candidates based on the presence of mutations in their coding regions and as per the RNA expression pattern during the inflorescence stage. Leaves and panicles obtained from plants harvested 5 days after heading showed differences in gene expression between Hwaseong and gw8.1-NILs. Most genes were upregulated in O. rufipogon and gw8.1-NIL than in Hwaseong. Scanning electron microscopy analysis of the lemma inner epidermal cells indicated that cell length was higher in gw8.1 NIL than in Hwaseong, indicating that gw8.1 might regulate cell elongation. Among the candidate genes, LOC_Os08g34380 encoding a putative receptor-like kinase and LOC_Os08g34550 encoding putative RING-H2 finger protein were considered as possible candidates based on their functional similarity.

Mesocotyl Elongation is Essential for Seedling Emergence Under Deep-Seeding Condition in Rice.

BACKGROUND: Direct-seeding cultivation by deep-seeding of seeds (drill seeding) is becoming popular due to the scarcity of land and labor. However, poor emergence and inadequate seedling establishment can lead to yield loss in direct-seeding cultivation by deep-sowing. In rice, mesocotyl and coleoptile are primarily responsible for seedling emergence from deeper levels of soil. RESULTS: Quantitative trait loci (QTLs) for mesocotyl and coleoptile length at 5-cm seeding depth were detected using 98 backcross inbred lines from a cross between Kasalath and Nipponbare. Three QTLs qMel-1, qMel-3, and qMel-6 for mesocotyl length were identified on chromosomes 1, 3, and 6, respectively, in two independent replicates. At two QTLs, qMel-1 and qMel-3, the Kasalath alleles increased mesocotyl length, whereas Nipponbare allele increased at qMel-6. The Nipponbare alleles at two QTLs (qCol-3 and qCol-5) increased the coleoptile length. Further, seeds of 54 chromosome segment substitution lines (CSSLs) from the cross between Kasalath and Nipponbare sown at 5 cm soil depth showed a significant positive correlation between seedling emergence and mesocotyl elongation (r > 0.6, P < 0.0001), but not with coleoptile elongation (r = 0.05, P = 0.7). Seedling emergence of Nipponbare, Kasalath, and the 3 of the 54 CSSLs rapidly decreased with increasing sowing depth. Seedling emergence at seeding depths of 7 and 10 cm was faster in Kasalath and CSSL-5 that harbored the Kasalath alleles across the qMel-1 and qMel-3 regions than in the other two CSSLs that contained a single QTL and Nipponbare alleles. CSSL-5 showed the longest mesocotyl among the 3 CSSLs, but no difference in coleoptile length was observed among the 3 CSSLs at seeding depths of 7 and 10 cm. CONCLUSION: Variation of mesocotyl elongation was found to be associated with seedling emergence at the seeding depth of 5 cm. To our knowledge, this is the first study performed using CSSLs to detect QTLs for mesocotyl or coleoptile elongation and to determine the effect of mesocotyl elongation on seedling emergence in rice. Our findings provides a foundation for developing rice cultivars that show higher seedling emergence after direct seeding by introgressing QTLs for mesocotyl elongation in rice breeding.

QTL Mapping of Grain Quality Traits Using Introgression Lines Carrying Oryza rufipogon Chromosome Segments in Japonica Rice.

BACKGROUND: Improved eating quality is a major breeding target in japonica rice due to market demand. Consequently, quantitative trait loci (QTL) for glossiness of cooked rice and amylose content associated with eating quality have received much research focus because of their importance in rice quality. RESULTS: In this study, QTL associated with 12 grain quality traits were identified using 96 introgression lines (IL) of rice developed from an interspecific cross between the Korean elite O. sativa japonica cultivar 'Hwaseong' and O. rufipogon over 7 years. QTL analyses indicated that QTL qDTH6 for heading date, detected on chromosome 6 is associated with variance in grain traits. Most QTLs detected in this study clustered near the qDTH6 locus on chromosome 6, suggesting the effect of qDTH6. O. rufipogon alleles negatively affected grain quality traits except for a few QTLs, including qGCR9 for glossiness of cooked rice on chromosome 9. To characterize the effect of the O. rufipogon locus harboring qGCR9, four lines with a single but different O. rufipogon segment near qGCR9 were compared to Hwaseong. Three lines (O. rufipopgon ILs) having O. rufipogon segment between RM242 and RM245 in common showed higher glossiness of cooked rice than Hwaseong and the other line (Hwaseong IL), indicating that qGCR9 is located in the 3.4-Mb region between RM242 and RM245. Higher glossiness of cooked rice conferred by the O. rufipogon allele might be associated with protein content considering that three lines had lower protein content than Hwaseong (P < 0.1). These three O. rufipogon ILs showed higher yield than Hwaseong and Hwaseong IL due to increase in spikelets per panicle and grain weight indicating the linkage of qGCR9 and yield component QTLs. CONCLUSION: The qGCR9 locus is of particular interest because of its independence from other undesirable grain quality traits in O. rufipogon. SSR markers linked to qGCR9 can be used to develop high-quality japonica lines and offer a starting point for map-based cloning of genes underlying this trait. To our knowledge, this is the first report to map a beneficial QTL for glossiness of cooked rice from a wild rice, O. rufipogon.