Transcriptomic Changes Induced by Drought Stress in Hardneck Garlic during the Bolting/Bulbing Stage

Garlic (Allium sativum L.) is an economically important, monocotyledonous plant with a strong taste and odor. Drought stress adversely affects its growth, development, and yield, particularly during the bolting/bulbing stage. Herein we performed RNA-seq to assess transcriptomic changes induced by drought stress in bolting/bulbing hardneck garlic plants (Purple Glazer). We observed that drought stress significantly reduced photosynthesis rate, fresh weight, and leaf water content. Transcriptomic analysis of garlic leaves under normal conditions and drought stress led to the identification of 5215 differentially expressed genes (2748 up- and 2467 downregulated). The upregulated DEGs were primarily involved in “biological process”, “metabolic process”, “oxidation-reduction process”, carbohydrate and lipid metabolism, and “proteolysis”, whereas the downregulated DEGs were mainly involved in “biological process” and metabolism of various molecules. In addition, genes encoding abscisic acid biosynthetic and catabolic enzymes, heat shock proteins, and E3 ubiquitin ligases were significantly altered by drought stress, indicating involvement in drought tolerance. A further comparison with the DEGs related to salinity stress-treated garlic revealed 867 and 305 DEGs with a similar and reverse expression alteration tendency, respectively.

Mandibular Structure, Gut Contents Analysis and Feeding Group of Orthopteran Species Collected from Different Habitats of Satoyama Area within Kanazawa City, Japan

A study was conducted on assemblies of various orthopteran species from distinct habitats in the Satoyama region, Kanazawa City, Ishikawa Prefecture, Japan, and a total of 50 distinct orthopteran species were registered. These species were represented by 10 families and were belonged to 17 subfamilies and 27 tribes. Results based on stereo-microscopic examination of the mandibular morphology and the analysis of gut contents suggested seven proposed feeding groups for these collected orthopteran species. Among the examined subfamilies, family Tettigoniidae proved to be the most diverse in mandibular structure and four feeding groups were assigned. This was followed by family Acrididae, which showed three feeding groups. Other families contained only single feeding group. It was noted that only five species, from family Acrididae, were graminivorous with their mandibles characterized by comparatively very short incisors and relatively wide molar regions. The analysis of gut contents of these five species proved to contain more than 80% monocotyledonous plant species. Predation and scavenging as feeding habits were also recorded in some orthopteran species.

Cloning of long sterile lemma (lsl2), a single recessive gene regulating spike germination in rice (Oryza sativa L.)

Background: Rice is a typical monocotyledonous plant and an important cereal crop. The structural units of rice flowers are spikelets and florets, and floral organ development and spike germination affect rice reproduction and yield.Results: In this study, we identified a novel long sterile lemma (lsl2) mutant from an EMS population. First, we mapped the lsl2 gene between the markers Indel7-22 and Indel7-27, which encompasses a 25-kb region. The rice genome annotation indicated the presence of four candidate genes in this region. Through gene prediction and cDNA sequencing, we confirmed that the target gene in the lsl2 mutant is allelic to LONG STERILE LEMMA1 (G1)/ELONGATED EMPTY GLUME (ELE), hereafter referred to as lsl2. Further analysis of the lsl2 and LSL2 proteins showed a one-amino-acid change, namely, the mutation of serine (Ser) 79 to proline (Pro) in lsl2 compared with LSL2, and this mutation might change the function of the protein. Knockout experiments showed that the lsl2 gene is responsible for the long sterile lemma phenotype. The lsl2 gene might reduce the damage induced by spike germination by decreasing the seed germination rate, but other agronomic traits of rice were not changed in the lsl2 mutant. Taken together, our results demonstrate that the lsl2 gene will have specific application prospects in future rice breeding.Conclusions: The lsl2 gene is responsible for the long sterile lemma phenotype and might reduce the damage induced by spike germination by decreasing the seed germination rate.

Cloning of long sterile lemma (lsl2), a single recessive gene that regulates spike germination in rice (Oryza sativa L.)

Background Rice is a typical monocotyledonous plant and an important cereal crop. The structural units of rice flowers are spikelets and florets, and floral organ development and spike germination affect rice reproduction and yield. Results In this study, we identified a novel long sterile lemma (lsl2) mutant from an EMS population. First, we mapped the lsl2 gene between the markers Indel7–22 and Indel7–27, which encompasses a 25-kb region. The rice genome annotation indicated the presence of four candidate genes in this region. Through gene prediction and cDNA sequencing, we confirmed that the target gene in the lsl2 mutant is allelic to LONG STERILE LEMMA1 (G1)/ELONGATED EMPTY GLUME (ELE), hereafter referred to as lsl2. Further analysis of the lsl2 and LSL2 proteins showed a one-amino-acid change, namely, the mutation of serine (Ser) 79 to proline (Pro) in lsl2 compared with LSL2, and this mutation might change the function of the protein. Knockout experiments showed that the lsl2 gene is responsible for the long sterile lemma phenotype. The lsl2 gene might reduce the damage induced by spike germination by decreasing the seed germination rate, but other agronomic traits of rice were not changed in the lsl2 mutant. Taken together, our results demonstrate that the lsl2 gene will have specific application prospects in future rice breeding. Conclusions The lsl2 gene is responsible for the long sterile lemma phenotype and might reduce the damage induced by spike germination by decreasing the seed germination rate.

Cloning of long sterile lemma (lsl2), a single recessive gene that regulates spike germination in rice (Oryza sativa L.)

Background: Rice is a typical monocotyledonous plant and an important cereal crop. The structural units of rice flowers are spikelets and florets, and floral organ development and spike germination affect rice reproduction and yield.Results: In this study, we identified a novel long sterile lemma (lsl2) mutant from an EMS population. First, we mapped the lsl2 gene between the markers Indel7-22 and Indel7-27, which encompasses a 25-kb region. The rice genome annotation indicated the presence of four candidate genes in this region. Through gene prediction and cDNA sequencing, we confirmed that the target gene in the lsl2 mutant is allelic to LONG STERILE LEMMA1 (G1)/ELONGATED EMPTY GLUME (ELE), hereafter referred to as lsl2. Further analysis of the lsl2 and LSL2 proteins showed a one-amino-acid change, namely, the mutation of serine (Ser) 79 to proline (Pro) in lsl2 compared with LSL2, and this mutation might change the function of the protein. Knockout experiments showed that the lsl2 gene is responsible for the long sterile lemma phenotype. The lsl2 gene might reduce the damage induced by spike germination by decreasing the seed germination rate, but other agronomic traits of rice were not changed in the lsl2 mutant. Taken together, our results demonstrate that the lsl2 gene will have specific application prospects in future rice breeding.Conclusions: The lsl2 gene is responsible for the long sterile lemma phenotype and might reduce the damage induced by spike germination by decreasing the seed germination rate.

Cloning of Long Sterile Lemma (lsl2), A Single Recessive Gene Regulating Spike Germination in Rice (Oryza Sativa L.)

Background: Rice is a typical monocotyledonous plant and an important cereal crop. The structural units of rice flowers are spikelets and florets. Floral organ development and spike germination affect rice reproduction and yield. Results: In this study, we identified a novel long sterile lemma (lsl2) mutant from an EMS population. First, we mapped the lsl2 gene between the markers Indel7-22 and Indel7-27, which encompasses a region of 25 kb. The rice genome annotation indicates the presence of four candidate genes in this region. Through gene prediction and cDNA sequencing, we confirmed that the target gene in the lsl2 mutant is allelic to LONG STERILE LEMMA1 (G1)/ELONGATED EMPTY GLUME (ELE), hereafter referred to as lsl2. Further analysis showed a one-amino acid change, serine (Ser) 79 mutated to proline (Pro), in the lsl2 protein had compared with LSL2, which may change the function of the LSL2 protein. The knockout experiments showed that the lsl2 gene is responsible for the long sterile lemma phenotype. The lsl2 gene may reduce the damage caused by spike germination by decreasing the seed germination rate, and yet other agronomic traits of rice are not affected in the lsl2 mutant. Taken together, our results demonstrate that the lsl2 gene will have specific application prospects in future rice breeding.Conclusions: The lsl2 gene is responsible for the long sterile lemma phenotype, and may reduce the damage caused by spike germination by decreasing the seed germination rate.

Transcriptome Assembly and Gene Expression Analysis of Leaf and Rhizome tissues of Dioscorea opposita

Background: Dioscorea opposita is a monocotyledonous plant in the Dioscoreaceae family. The rhizome of D. opposita, known as “dioscoreae rhiaoma” or “Chinese yam”, is not only a well-known traditional Chinese medicine, but also a popular health food.Methods:In this study, the leaf and rhizome tissues of D. opposita were collected. Their transcriptome sequenceand were obtained using an Illumina Hiseq 4000 platform. The data was analyzed by bioinformatics software. Likewise, the consistent expression pattern of DEGs was validated with qRT-PCR analysis.Results: A total of 46,982,031 and 53,689,620 clean reads from leaf and rhizome tissues were acquired, respectively (SRP: PRJNA628588). 50,765 unigenes were obtained with an average length of 1050 base pairs (bp). A total of 13,259 significant differentially expressed genes (DEGs) were obtained from leaf versus rhizome tissues, including 5536 up-regulated and 7723 down-regulated unigenes. In addition, 20,607 simple sequence repeats (SSRs) were identified in this study. Conclusions:This study not only enriched the transcriptomic data of D. opposita, but also laid a foundation for the analysis of terpenoid synthesis pathway.