HD2 Genes Research Articles

Homeodomain 1 Genes of the Different HD Subloci of Flammulina velutipes Can Activate the HD Pathway and Are Involved in Mating, Clamp Cell Formation, and Upregulation of FvClp1.

Flammulina velutipes has two independent and functional mating type factors, HD and PR. The HD locus contains two separate subloci: HD-a and HD-b. In this study, we investigated the roles of Hd1 genes of the HD-a and HD-b subloci in the process of mating, clamp cell formation, and regulation of FvClp1 (F. velutipes clampless1 gene) gene expression in F. velutipes. To this end, we introduced Hd1 genes from mating compatible strains into F. velutipes monokaryon L11. Overexpression of Hd1 gene FvHd-a1-1 of the HD-a sublocus resulted in the formation of pseudoclamps in L11 monokaryons. L11 mutants overexpressing the Hd1 gene FvHd-b1-2 of the HD-b sublocus also similarly developed pseudoclamps in the L11 monokaryons. Moreover, these mutant L11 monokaryons produced complete clamps when crossed with monokaryotic strains that differed at the PR loci, i.e., when selective activation of the PR pathway was obtained through crossing. Thus, Hd1 genes of the two different HD subloci in F. velutipes can activate the HD mating type pathway and induce clamp cell formation. In addition, activation of the HD pathway resulted in upregulation of the FvClp1 gene. Finally, to complete clamp cell formation, activation of the PR pathway appears to be essential. Overall, these findings were beneficial for deepening our understanding of sexual reproduction and fruiting body development of edible fungi.

Comparative Structural Analysis of The Homeodomain Protein in the Bipolar Basidiomycete, Mycoleptodonoides aitchisonii (Bunaharitake)

Mycoleptodonoides aitchisonii is a bipolar mushroom with monokaryons can form clamp cells, regardless of the mating type. Previously, only HD2-18 was identifi ed and characterized at the A locus of Maspi18 (A1). In this study, unlike the A locus in strain Maspi18, HD1-7-like gene (Mahd1-7) and HD2-7 gene (Mahd2-7) were identifi ed at the A locus of the compatible strain Maspi7 (A2), but the nine fl anking genes were highly conserved, suggesting that recombination events may have occurred between HD1 and HD2 genes over evolutionary time. Following phylogenetic and HD protein structural comparisons with other basidiomycetes, homeodomains were identifi ed in HD2-7 and HD2-18, but the former lacked nuclear localization signals (NLS) whereas the latter, like the HD1-7-like protein, did not. These fi ndings indicated that one homeodomain and several NLS on the same or different HD proteins is the minimum suffi cient for driving clamp cell formation in M. aitchisonii. The fi ndings implied that over evolutionary time, unlike HD2, the homeodomain in HD1 does not play a major role in clamp cell formation, and that HD1-7 performs the function of carrying the NLS. Herein, we propose a new hypothesis for clamp cell formation in M. aitchisonii. The fi ndings of this study provide a foundation for understanding the role of heterokaryonization in basidiomycete mushrooms.

Crop Evolution of Foxtail Millet.

Studies on the domestication, genetic differentiation, and crop evolution of foxtail millet are reviewed in this paper. Several genetic studies were carried out to elucidate the genetic relationships among foxtail millet accessions originating mainly from Eurasia based on intraspecific hybrid pollen semi-sterility, isozymes, DNA markers, and single-nucleotide polymorphisms. Most studies suggest that China is the center of diversity of foxtail millet, and landraces were categorized into geographical groups. These results indicate that this millet was domesticated in China and spread over Eurasia, but independent origin in other regions cannot be ruled out. Furthermore, the evolution of genes was reviewed (i.e., the Waxy gene conferring amylose content in the endosperm, the Si7PPO gene controlling polyphenol oxidase, the HD1 and SiPRR37 genes controlling heading time, the Sh1 and SvLes1 genes involved in grain shattering, and the C gene controlling leaf sheath pigmentation), and the variation and distribution of these genes suggested complex patterns of evolution under human and/or natural selection.

Effects of the core heading date genes Hd1, Ghd7, DTH8, and PRR37 on yield-related traits in rice.

We clarify the influence of the genotypes of the heading date genes Hd1, Ghd7, DTH8, and PRR37 and their combinations on yield-related traits and the functional differences between different haplotypes. Heading date is a key agronomic trait in rice (Oryza sativa L.) that determines yield and adaptability to different latitudes. Heading date 1 (Hd1), Grain number, plant height, and heading date 7 (Ghd7), Days to heading on chromosome 8 (DTH8), and PSEUDO-RESPONSE REGULATOR 37 (PRR37) are core rice genes controlling photoperiod sensitivity, and these genes have many haplotypes in rice cultivars. However, the effects of different haplotypes at these genes on yield-related traits in diverse rice materials remain poorly characterized. In this study, we knocked out Hd1, Ghd7, DTH8, or PRR37, alone or together, in indica and japonica varieties and systematically investigated the agronomic traits of each knockout line. Ghd7 and PRR37 increased the number of spikelets and improved yield, and this effect was enhanced with the Ghd7 DTH8 or Ghd7 PRR37 combination, but Hd1 negatively affected yield. We also identified a new weak functional Ghd7 allele containing a mutation that interferes with splicing. Furthermore, we determined that the promotion or inhibition of heading date by different PRR37 haplotypes is related to PRR37 expression levels, day length, and the genetic background. For rice breeding, a combination of functional alleles of Ghd7 and DTH8 or Ghd7 and PRR37 in the hd1 background can be used to increase yield. Our study clarifies the effects of heading date genes on yield-related traits and the functional differences among their different haplotypes, providing valuable information to identify and exploit elite haplotypes for heading date genes to breed high-yielding rice varieties.

Structure Analysis of the MatA Locus of Sexual Compatibility in the Edible Mushroom Pleurotus ostreatus

The edible oyster mushroom Pleurotus ostreatus is one of the most cultivated species worldwide. Morphogenesis associated with the maturation of fruit bodies is controlled by two unlinked loci of sexual compatibility matA and matB with multiple alleles (tetrapolar system of sexual compatibility). Quantitative analysis of the alleles of mating compatibility loci in 17 natural isolates collected in the Moscow region was performed in mon–mon (monokaryons–monokaryon) and di–mon (dikaryon–monokaryon) crossings. Four monokaryotic testers strains which were heteroallelic at both mating type loci were obtained for each of the five natural mushroom isolates by using original technique of sterile spore prints on Petri dishes and mon–mon crossing. Twelve natural isolates were crossed via di-mon mating with the four monokaryotic testers M-38. Genetic analysis of the alleles of sexual compatibility loci in 17 natural isolates revealed multiple alleles at both loci: at least ten alleles at matA locus and eight alleles at matB locus. Structural organization analysis of the matA locus was performed in silico for homokaryotic strains PC9 and PC15 based on the whole-genome sequencing data available at DOE Joint Genome Institute. The matA locus has an extremely divergent structure: there are one copy of the homeodomain gene hd1 and one copy of the hd2 gene in the PC9 strain, whereas the matA locus of the PC15 strain is composed by two copies of hd1.1 and hd1.2 genes (class HD1 homeodomain proteins) and one copy of hd2 gene (class HD2 proteins). Comprehensive analysis of amino acid sequences of HD1 and HD2 homeodomain proteins demonstrated that the proteins have a globular structure with the nuclear localization and contain a variable N-terminus and a more conserved DNA-binding domain with a specific conserved motif WFXNXR in the third ɑ-helix. The results suggest that multiple alleles of the matA locus of sexual compatibility in basidiomycete fungi is achieved due to both different copy number of the coding hd genes within the locus and the variability of the coding gene sequences.

Complete genome sequences and comparative secretomic analysis for the industrially cultivated edible mushroom Lyophyllum decastes reveals insights on evolution and lignocellulose degradation potential.

Lyophyllum decastes, also known as Luronggu in China, is a culinary edible and medicinal mushroom that was widely cultivated in China in recent years. In the present study, the complete high-quality genome of two mating compatible L. decastes strain was sequenced. The L. decastes LRG-d1-1 genome consists of 47.7 Mb in 15 contigs with a contig N90 of 2.08 Mb and 14,499 predicted gene models. Phylogenetic analysis revealed that L. decastes exhibits a close evolutionary relationship to the Termitomyces and Hypsizygus genus and was diverged from H. marmoreus ~ 45.53 Mya ago. Mating A loci of L. decastes compose of five and four HD genes in two monokaryotic strains, respectively. Mating B loci compose of five STE genes in both two monokaryotic strains. To accelerate the cross-breeding process, we designed four pairs of specific primers and successfully detected both mating types in L. decastes. As a wood-rotting mushroom, a total of 541 genes accounting for 577 CAZymes were identified in the genome of L. decastes. Proteomic analysis revealed that 1,071 proteins including 182 CAZymes and 258 secreted enzymes were identified from four groups (PDB, PDB + bran, PDB + cotton hull, and PDB + sawdust). Two laccases and a quinone reductase were strongly overproduced in lignin-rich cultures, and the laccases were among the top-3 secreted proteins, suggesting an important role in the synergistic decomposition of lignin. These results revealed the robustness of the lignocellulose degradation capacity of L. decastes. This is the first study to provide insights into the evolution and lignocellulose degradation of L. decastes.

Structure Analysis of the <i>MatA</i> Locus of Sexual Compatibility in the Edible Mushroom <i>Pleurotus ostreatus</i>

The edible oyster mushroom Pleurotus ostreatus is one of the most cultivated species worldwide. Morphogenesis associated with the fruit bodies maturation is controlled by two unlinked loci of sexual compatibility matA and matB with multiple alleles (tetrapolar system of sexual compatibility). Quantitative analysis of the alleles of mating compatibility loci in 17 natural isolates collected in the Moscow region was performed in mon-mon (monokaryon – monokaryon) and di-mon (dikaryon – monokaryon) crossings. Four monokaryotic testers strains which were heteroallelic at both mating type loci were obtained for each of the five natural mushroom isolates by using original technique of sterile spore prints on Petri dishes and mon-mon crossing. Twelve natural isolates were crossed via di-mon mating with the four monokaryotic testers M-38. Genetic analysis of the alleles of sexual compatibility loci in 17 natural isolates revealed multiple alleles at both loci: at least 10 alleles at matA locus and eight alleles at matB locus. Structural organization analysis of the matA locus was performed in silico for homokaryotic strains PC9 and PC15 based on the genome sequencing data available at DOE Joint Genome Institute. The matA locus is proved to be of extremely divergent structure: there are one copy of the homeodomain gene hd1 and one copy of the hd2 gene in the PC9 strain, whereas the matA locus of the PC15 strain is composed by two copies of hd1.1 and hd1.2 genes (class HD1 homeodomain proteins) and one copy of hd2 gene (class HD2 proteins). Comprehensive analysis of amino acid sequences of HD1 and HD2 homeodomain proteins demonstrated that the proteins have a globular structure with the nuclear localization and contain a variable N-terminus and the more conservative DNA-binding domain with a specific conservative motif WFXNXR in the third ɑ-helix. The results approve the opinion that multiple alleles of the matA locus of sexual compatibility in basidiomycete fungi is achieved by different copies’ number of the coding hd genes within the locus, as well as by the variability of the coding gene sequences.

GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North Korea.

Heading date (Hd) is one of the main factors determining rice production and regional adaptation. To identify the genetic factors involved in the wide regional adaptability of rice, we conducted a genome-wide association study (GWAS) with 190 North Korean rice accessions selected for non-precocious flowering in the Philippines, a low-latitude region. Using both linear mixed models (LMM) and fixed and random model circulating probability unification (FarmCPU), we identified five significant loci for Hd in trials in 2018 and 2019. Among the five lead single nucleotide polymorphisms (SNPs), three were located adjacent to the known Hd genes, Heading date 3a (Hd3a), Heading date 5 (Hd5), and GF14-c. In contrast, three SNPs were located in novel loci with minor effects on heading. Further GWAS analysis for photoperiod insensitivity (PS) revealed no significant genes associated with PS, supporting that this North Korean (NK) population is largely photoperiod-insensitive. Haplotyping analysis showed that more than 80% of the NK varieties harbored nonfunctional alleles of major Hd genes investigated, of which a nonfunctional allele of Heading date 1 (Hd1) was observed in 66% of the varieties. Geographical distribution analysis of Hd allele combination types showed that nonfunctional alleles of floral repressor Hd genes enabled rice cultivation in high-latitude regions. In contrast, Hd1 alleles largely contributed to the wide regional adaptation of rice varieties. In conclusion, an allelic combination of Hd genes is critical for rice cultivation across wide areas.

Whole-genome sequence of a high-temperature edible mushroom Pleurotus giganteus (zhudugu).

Most of the sequenced wood-rotting edible mushroom produce fruiting body at relatively low temperatures. Little information has been known about the high-temperature wood-rotting mushroom. Here, we performed de novo sequencing and assembly of the genome of a high-temperature edible mushroom Pleurotus giganteus from a monokaryotic strain zhudugu2 using the Illumina and Pac-Bio CLR sequencing technologies. P. giganteus, also known as Zhudugu in China, is a well-known culinary edible mushroom that has been widely distributed and cultivated in China, Southeast Asia, and South Asia. The genome consists of 40.00 Mb in 27 contigs with a contig N50 of 4.384 Mb. Phylogenetic analysis reveals that P. giganteus and other strains in Pleurotus clustered in one clade. Phylogenetic analysis and average nucleotide identity analysis indicated that the P. giganteus genome showed a closer relationship with other Pleurotus species. Chromosome collinearity analysis revealed a high level of collinearity between P. ostreatus and P. giganteus. There are 12,628 protein-coding genes annotated in this monoploid genome. A total of 481 enzymes accounting for 514 carbohydrate-active enzymes (CAZymes) terms were identified in the P. giganteus genome, including 15 laccases and 10 class II peroxidases predicted in the genome, which revealed the robustness of lignocellulose degradation capacity of P. giganteus. The mating-A type locus of P. giganteus consisted of a pair of homeodomain mating-type genes HD1 and HD2. The mating-B type locus of P. giganteus consisted of at least four pheromone receptor genes and three pheromone genes. The genome is not only beneficial for the genome-assisted breeding of this mushroom but also helps us to understand the high-temperature tolerance of the edible mushroom.

Austropuccinia psidii uses tetrapolar mating and produces meiotic spores in older infections on Eucalyptus grandis

Austropuccinia psidii is the causal agent of myrtle rust, a fungal disease that infects over 480 species in the Myrtaceae. A. psidii is a biotrophic pathogen that reproduces sexually and asexually. Sexual reproduction has been previously shown on Syzygium jambos and little is known about its reproductive biology on other hosts or whether populations that were formerly structured by host range can outcross on universally susceptible hosts. We investigated if mating genes in three genomes of A. psidii were under selection as a proxy for whether different strains can reproduce sexually on a shared host. We examined three homologs of the STE3.2 gene, sequences of which were near-identical in the three genomes, and the homeodomain locus, which contained two alleles of two homeodomain genes in each genome. A. psidii likely uses tetrapolar mating. Pheromone/receptor loci were distal to homeodomain loci, and based on haplotypes of a phased assembly, mate compatibility is regulated by multiallelic HD genes and biallelic STE3.2 genes; the third homolog of STE3.2 (STE3.2-1) was present in both haplotypes, and our study supports hypotheses this gene does not regulate mate recognition. Populations of A. psidii formerly structured by host range could potentially outcross on universal hosts based on their related mating genes, however this hypothesis should remain theoretical given the implications for biosecurity. Additionally, we searched for core meiotic genes in genomes of A. psidii, four species of Puccinia, and Sphaerophragmium acaciae through comparative genomics based on 136 meiosis-related orthologous genes modeled from Mycosarcoma maydis. Meiotic genes are conserved in rust fungi at family rank. We analyzed the expression of two meiotic and four mitotic genes of A. psidii on E. grandis over a 28-day time course to validate that identified meiotic genes were upregulated in teliospores. Three mitotic genes were significantly downregulated in samples collected 28 days after inoculation (DAI) compared to 14 DAI. Expression of meiotic genes was significantly up-regulated in samples collected 28 DAI compared to 14 DAI, indicating a temporal switch from production of uredinia (mitotic stage) to telia in the life cycle, which we hypothesize may be in response to leaf ageing.

Hd1, Ghd7, and DTH8 synergistically determine the rice heading date and yield-related agronomic traits

Heading date determines the seasonal and regional adaptation of rice (Oryza sativa L.) varieties and is mainly controlled by photoperiod sensitivity (PS). The core heading date genes Hd1, Ghd7, DTH8, and PRR37 act synergistically in regulating the PS. In this study, we systematically analyze the heading date, PS, and agronomic traits of eight homozygous lines with various combinations of Hd1, Ghd7, and DTH8 alleles in the prr37 background under long-day (LD) and short-day (SD) conditions, respectively. We find that Hd1 alone promotes heading, regardless of the day length. However, under LDs, Hd1 suppresses flowering, in coordination with functional Ghd7 or with Ghd7 and DTH8. These loci cooperate to negatively regulate the Ehd1-Hd3a/RFT1 pathway and delay heading. Under SDs, Hd1 competes with various heading suppressors to promote heading. Therefore, the dual function of Hd1 is vital for PS. The lines carrying Hd1 alone show reduced plant height with fewer primary and secondary branches in panicles. Lines carrying Ghd7 and DTH8 (with hd1) show delayed heading and improve agronomic traits. Overall, our results reveal the regulation of rice PS flowering by the core heading date genes and their effects on agronomic traits, providing valuable information for the selection of rice varieties for adaptation to different light and temperature conditions.

Real-Time Monitoring of Key Gene Products Involved in Rice Photoperiodic Flowering.

Flowering is an important biological process through which plants determine the timing of reproduction. In rice, florigen mRNA is induced more strongly when the day length is shorter than the critical day length through recognition of 30-min differences in the photoperiod. Grain number, plant height, and heading date 7 (Ghd7), which encodes a CCT-domain protein unique to monocots, has been identified as a key floral repressor in rice, and Heading date 1 (Hd1), a rice ortholog of the Arabidopsis floral activator CONSTANS (CO), is another key floral regulator gene. The Hd1 gene product has been shown to interact with the Ghd7 gene product to form a strong floral repressor complex under long-day conditions. However, the mRNA dynamics of these genes cannot explain the day-length responses of their downstream genes. Thus, a real-time monitoring system of these key gene products is needed to elucidate the molecular mechanisms underlying accurate photoperiod recognition in rice. Here, we developed a monitoring system using luciferase (LUC) fusion protein lines derived from the Ghd7-LUC and Hd1-LUC genes. We successfully obtained a functionally complemented gene-targeted line for Ghd7-LUC. Using this system, we found that the Ghd7-LUC protein begins to accumulate rapidly after dawn and reaches its peak more rapidly under a short-day condition than under a long-day condition. Our system provides a powerful tool for revealing the accurate time-keeping regulation system incorporating these key gene products involved in rice photoperiodic flowering.

Genetic structure and evolutionary diversity of mating-type (MAT) loci in\xa0Hypsizygus marmoreus

The mating compatibility in fungi is generally governed by genes located within a single or two unlinked mating type (MAT) loci. Hypsizygus marmoreus is an edible mushroom in the order Agaricales with a tetrapolar system, which contains two unlinked MAT loci-homeodomain (HD) transcription factor genes and pheromone/pheromone receptor genes (P/R). In this study, we analyzed the genetic structure and diversity of MAT loci in tetrapolar system of H. marmoreus through sequencing of 54 heterokaryon and 8 homokaryon strains. Although within the HD loci, the gene order was conserved, the gene contents were variable, and the HD loci haplotypes were further classified into four types. By analyzing the structure, phylogeny, and the HD transmissibility based on the progeny of these four HD mating-type loci types, we found that they were heritable and tightly linked at the HD loci. The P/R loci genes were found to comprise three pheromone receptors, three pheromones, and two pheromone receptor-like genes. Intra- and inter-specific phylogenetic analyses of pheromone receptors revealed that the STE3 genes were divided into three groups, and we thus theorize that they diverged before speciation. Comparative analysis of the MAT regions among 73 Basidiomycete species indicated that the diversity of HD and P/R loci in Agaricales and Boletales may contribute to mating compatibility. The number of HD genes were not correlated with the tetrapolar or bipolar systems. In H. marmoreus, the expression levels of these genes at HD and P/R loci of compatible strains were found higher than in those of homonuclear/homokaryotic strains, indicating that these mating genes acted as switches for mating processes. Further collinear analysis of HD loci in interspecific species found that HD loci contains conserved recombination hotspots showing major rearrangements in Coprinopsis cinerea and Schizophyllum commune, suggesting different mechanisms for evolution of physically linked MAT loci in these groups. It seems likely that gene rearrangements are common in Agaricales fungi around HD loci. Together, our study provides insights into the genomic basis of mating compatibility in H. marmoreus.

High Ambient Temperatures Inhibit Ghd7-Mediated Flowering Repression in Rice.

The anticipation of changing seasons is crucial for reproduction in plants. Despite the broad cultivation area, the effects of ambient temperature on photoperiodic flowering are largely unknown in rice. Here, we first examined flowering time under four distinct conditions: short-day or long-day and high or low temperature, using cultivars, nearly isogenic lines, and mutants in rice. We also examined gene expression patterns of key flowering-time genes using the same lines under various conditions including temporal dynamics after light pulses. In addition to delayed flowering because of low growth rates, we found that photoperiodic flowering is clearly enhanced by both Hd1 and Ghd7 genes under low-temperature conditions in rice. We also revealed that PhyB can control Ghd7 repressor activity as a temperature sensor to inhibit Ehd1, Hd3a and RFT1 at lower temperatures, likely through a post-transcriptional regulation, despite inductive photoperiod conditions. Furthermore, we found that rapid reduction of Ghd7 messenger RNA (mRNA) under high-temperature conditions can lead to mRNA increase in a rice florigen gene, RFT1. Thus, multiple temperature-sensing mechanisms can affect photoperiodic flowering in rice. The rising of ambient temperatures in early summer likely contributes to the inhibition of Ghd7 repressor activity, resulting in the appropriate floral induction of rice in temperate climates.

Mating-Type Locus Organization and Mating-Type Chromosome Differentiation in the Bipolar Edible Button Mushroom Agaricus bisporus.

In heterothallic basidiomycete fungi, sexual compatibility is restricted by mating types, typically controlled by two loci: PR, encoding pheromone precursors and pheromone receptors, and HD, encoding two types of homeodomain transcription factors. We analysed the single mating-type locus of the commercial button mushroom variety, Agaricus bisporus var. bisporus, and of the related variety burnettii. We identified the location of the mating-type locus using genetic map and genome information, corresponding to the HD locus, the PR locus having lost its mating-type role. We found the mip1 and β-fg genes flanking the HD genes as in several Agaricomycetes, two copies of the β-fg gene, an additional HD2 copy in the reference genome of A. bisporus var. bisporus and an additional HD1 copy in the reference genome of A. bisporus var. burnettii. We detected a 140 kb-long inversion between mating types in an A. bisporus var. burnettii heterokaryon, trapping the HD genes, the mip1 gene and fragments of additional genes. The two varieties had islands of transposable elements at the mating-type locus, spanning 35 kb in the A. bisporus var. burnettii reference genome. Linkage analyses showed a region with low recombination in the mating-type locus region in the A. bisporus var. burnettii variety. We found high differentiation between β-fg alleles in both varieties, indicating an ancient event of recombination suppression, followed more recently by a suppression of recombination at the mip1 gene through the inversion in A. bisporus var. burnettii and a suppression of recombination across whole chromosomes in A. bisporus var. bisporus, constituting stepwise recombination suppression as in many other mating-type chromosomes and sex chromosomes.

Deciphering variation of 239 elite japonica rice genomes for whole genome sequences-enabled breeding

Revealing genomic variation of representative and diverse germplasm is the cornerstone of deploying genomics information into genetic improvement programs of species of agricultural importance. Here we report the re-sequencing of 239 japonica rice elites representing the genetic diversity of japonica germplasm in China, Japan and Korea. A total of 4.8 million SNPs and PAV of 35,634 genes were identified. The elites from Japan and Korea are closely related and relatively less diverse than those from China. A japonica rice pan-genome was constructed, and 35 Mb non-redundant novel sequences were identified, from which 1131 novel genes were predicted. Strong selection signals of genomic regions were detected on most of the chromosomes. The heading date genes Hd1 and Hd3a have been artificially selected during the breeding process. The results from this study lay the foundation for future whole genome sequences-enabled breeding in rice and provide a paradigm for other species.

Mapping of a Major QTL, <i>qHD6-SD</i> Responsible for Days to heading Under Natural Short Day Conditions to Develop Rice Varieties adaptable to Tropical Regions

In the tropics (Southeast Asian countries), indica rice is more common than japonica. Japonica rice is mainly cultivated in temperate regions, including Korea, Japan, and China (northeast regions) due to its poor adaptation to tropical areas. To develop tropically-adapted high-yielding japonica rice, breeders should overcome the challenges, including extremely early flowering, low biomass accumulation, and inferior panicle traits. This study investigated 180 F9 recombinant inbred lines (RILs) developed from a cross between Ilpum (temperate japonica) and Zenith (indica) as a case population to identify quantitative trait loci (QTLs) that influence the said traits. Here we identified two major QTLs, qHD6-SD and qHD6- LD, conferring days to heading under short day (SD) and long day (LD) conditions, respectively. Finer mapping revealed that both qHD6-SD and qHD6-LD located in the similar 98 kb region harbored the Hd1 gene. Days to heading in the RILs harboring the Zenith allele type of qHD6-SD under SD conditions were significantly longer than those in the RILs harboring the Ilpum allele type. On the contrary, days to heading in the RILs harboring the Zenith allele type of qHD6-SD under LD conditions were significantly shorter than those in the RILs harboring the Ilpum allele type. This bi-functionality of qHD6-SD upon heading strongly support the claim that both qHD6-SD and qHD6-LD might be the Hd1 gene. Our findings further support the claim that the functional allele type of Hd1 gene delays long-day heading and promotes extremely early short-day heading. Therefore, a non-functional Hd1 type is critical to tropical adaptation of japonica rice since it delays the heading date, which is essential to attain prolonged vegetative state in order to achieve optimum biomass, increased spikelet number, and grain filling capacity.

Identification of a Potential Gene for Elevating ω-3 Concentration and Its Efficiency for Improving the ω-6/ω-3 Ratio in Soybean.

This present study was to identify a novel candidate gene that contributes to the elevated α-linolenic acid (ALA, ω-3) concentration in PE2166 from mutagenesis of Pungsannamul. Major loci qALA5_1 and qALA5_2 were detected on chromosome 5 of soybean through quantitative trait loci mapping analyses of recombinant inbred lines. With next-generation sequencing of parental lines and Pungsannamul and recombinant analyses, a potential gene, Glyma.05g221500 (HD), controlling elevated ALA concentration was identified. HD is a homeodomain-like transcriptional regulator that may regulate the expression level of microsomal ω-3 fatty acid desaturase (FAD3) genes responsible for the conversion of linoleic acid into ALA in the fatty acid biosynthetic pathway. In addition, we hypothesized that a combination of mutant alleles, HD, and either of microsomal delta-12 fatty acid desaturase 2-1 (FAD2-1) could reduce the ω-6/ω-3 ratio. In populations where HD, FAD2-1A, and FAD2-1B genes were segregated, a combination of a hd allele from PE2166 and either of the variant FAD2-1 alleles was sufficient to reduce the ω-6/ω-3 ratio in seeds.

Gene Pyramiding for Brown Planthopper Resistance-related Traits, Early Maturity and Aroma of Rice Assisted by Molecular and Phenotypic Markers

The brown planthopper (BPH)-resistant rice, early maturity, and aromatic are expected by both farmers and consumers. The traits have been combined through gene pyramiding and some promising rice genotypes obtained. However the genetic control of BPH resistance and maturity is quantitatively inherited, it is therefore both molecular and phenotypic assessments would be tremendously helpful in selecting promising genotypes. The study aimed to obtain genotypes with such valuable traits. Rice lines were analyzed using molecular markers i.e., RM586, RM589, RM8213 (BPH resistant gene markers); RM7610 and RM19414 (early maturity markers), and IFAP (Internal Fragrant Antisense Primer) for detecting aromatic, and INSP (Internal Non-fragrant Sense Primer) for non-aromatic rice. Phenotypic assessment was performed for brown planthopper resistant-related traits, such as chlorophyll content, stomatal conductance, and trichome density. Other evaluations were heading date and aroma (using 1.7% KOH solution). Results showed that molecular markers for evaluating BPH resistance genes (Bph3, Bph4, Qbph4, and Bph17), aroma (fgr gene), and heading date (Hd2 and Hd3 genes) could differentiate genotypes, and they serve as perfect markers, except for heading date markers. Seven genotypes i.e., #2, #3, #4, #5, #6, #10, and #11 were related to all traits expected based on molecular marker analysis. Meanwhile, genotypes #1, #2, #4, #6, and #11 were similar to their parents based on phenotypic analysis. Pyramiding program based on molecular and phenotypic markers enables us to combine three valuable traits into one rice genotype as presented in this study

Sequence Variants Linked to Key Traits in Interspecific Crosses between African and Asian Rice.

Asian and African rice gene pools vary in many traits that are important in rice breeding. The genetic basis of these differences was evaluated by analysis of important agronomic traits in crosses between African and Asian rice. Trait-associated variants (TAVs) influencing three quantitative agronomic traits, heading date (Hd), tiller number at maturity (T), and 1000 grain weight (TGW), were identified by association analysis of crosses between Asian and African rice. Populations were developed by crossing WAB56-104 (Oryza sativa) and CG14 (Oryza glaberrima). DNA from plants with extremely high or low values for these phenotypes was bulked and sequenced. The reference genome of O. sativa cv Nipponbare was used in general association analysis and candidate gene analysis. A total of 5152 non-synonymous single nucleotide polymorphisms (SNPs) across 3564 genes distinguished the low and the high bulks for Hd, T, and TGW traits; 611 non-synonymous SNPs across 447 genes were found in KEGG pathways. Six non-synonymous SNPs were found in the sequences of LOC107275952, LOC4334529, LOC4326177, LOC107275432, LOC4335790, and LOC107275425 genes associated with Hd, T, and TGW traits. These genes were involved in: abscisic-acid biosynthesis, carotenoid biosynthesis, starch and sucrose metabolism, and cytokinin biosynthesis. Analysis of 24 candidate genes associated with Hd, T, and TGW traits showed seven non-synonymous variations in the sequence of Hd3a and Ehd2 from the Hd genes (not in a KEGG pathway), D10 and D53 from the T genes (strigolactones biosynthetic pathway), and Gn1a and GIF1 from the TGW genes (cytokinin biosynthetic and starch and sucrose metabolism pathways). This study identified significant differences in allele frequencies supported by high sequence depth in analysis of bulks displaying high and low values for these key traits. These trait-associated variants are likely to be useful in rice improvement.