Genome-wide identification and characterization of SRLK gene family reveal their roles in self-incompatibility of Erigeron breviscapus.

Self-incompatibility (SI) is a reproductive protection mechanism that plants acquired during evolution to prevent self-recession. As the female determinant of SI specificity, SRK has been shown to be the only recognized gene on the stigma and plays important roles in SI response. Asteraceae is the largest family of dicotyledonous plants, many of which exhibit self-incompatibility. However, systematic studies on SRK gene family in Asteraceae are still limited due to lack of high-quality genomic data. In this study, we performed the first systematic genome-wide identification of S-locus receptor like kinases (SRLKs) in the self-incompatible Asteraceae species, Erigeron breviscapus, which is also a widely used perennial medicinal plant endemic to China.52 SRLK genes were identified in the E. breviscapus genome. Structural analysis revealed that the EbSRLK proteins in E. breviscapus are conserved. SRLK proteins from E. breviscapus and other SI plants are clustered into 7 clades, and the majority of the EbSRLK proteins are distributed in Clade I. Chromosomal and duplication analyses indicate that 65% of the EbSRLK genes belong to tandem repeats and could be divided into six tandem gene clusters. Gene expression patterns obtained in E. breviscapus multiple-tissue RNA-Seq data revealed differential temporal and spatial features of EbSRLK genes. Among these, two EbSRLK genes having high expression levels in tongue flowers were cloned. Subcellular localization assay demonstrated that both of their fused proteins are localized on the plasma membrane. All these results indicated that EbSRLK genes possibly involved in SI response in E. breviscapus. This comprehensive genome-wide study of the SRLK gene family in E. breviscapus provides valuable information for understanding the mechanism of SSI in Asteraceae.

Genetic Diversity and Association Mapping of Grain-Size Traits in Rice Landraces from the Honghe Hani Rice Terraces System in Yunnan Province.

The Honghe Hani Rice Terraces System (HHRTS) of Yunnan Province is an important agricultural and cultural heritage landscape. Until now, a large number of local rice landraces have been planted. Mining excellent genes contained in these landraces provides a reference for variety improvement and new variety breeding. In this study, 96 rice landraces collected from the Hani terraces were planted in Honghe Mengzi, Yunnan Province, in 2013, 2014, 2015, and 2021, and five major grain traits were measured and analyzed. The genomic variation of 96 rice landraces was scanned by 201 simple sequence repeat (SSR) markers. The genetic diversity, population structure, and genetic relationships of the natural population were analyzed. The mixed linear model (MLM) method of the TASSEL software was used to analyze the associations between markers and traits. A total of 936 alleles were amplified by 201 pairs of SSR primers. The average number of observed alleles (Na), the effective number of alleles (Ne), Shannon's information index (I), heterozygosity (H), and the polymorphism information content (PIC) per marker were 4.66, 2.71, 1.08, 0.15, and 0.55, respectively. Ninety-six landraces were divided into two groups by population structure, clustering, and principal component analysis, and indica rice was the main group. The coefficients of variation of the five traits ranged from 6.80 to 15.24%, and their broad heritabilities were more than 70%. In addition, there were positive correlations among the same grain traits between different years. Through MLM analysis, 2, 36, 7, 7, and 4 SSR markers were significantly associated with grain length (GL), grain width (GW), grain thickness (GT), grain length-width ratio (LWR), and thousand-grain weight (TGW), respectively. The explanation rates of phenotypic variation were 16.31 (RM449, Chr. 1)-23.51% (RM316, Chr. 9), 10.84 (RM523, Chr. 3; RM161/RM305, Chr. 5)-43.01% (RM5496, Chr. 1), 11.98 (RM161/RM305, Chr. 5)-24.72% (RM275, Chr. 6), 12.68 (RM126, Chr. 8)-36.96% (RM5496, Chr. 1), and 17.65 (RM4499, Chr. 2)-26.32% (RM25, Chr. 8), respectively. The associated markers were distributed on 12 chromosomes of the genome.

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae).

BACKGROUND: Amomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from different A. tsaoko tissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers. RESULTS: A total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism in A. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72 A. tsaoko accessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the six A. tsaoko populations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species. CONCLUSIONS: Our study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.

Analysis of the correlation of the expression level of hypoxia-inducible factor-1α with the glycosylation of oral squamous cell carcinoma.

OBJECTIVE: To investigate the correlation of the expression level of hypoxia-inducible factor-1α (HIF-1α) with the glycosylation of oral squamous cell carcinoma (OSCC). METHODS: We conducted an immunohistochemical SP method to detect the expression levels of HIF-1α and O-glycosylation-related proteins (O-linked N-acetylglucosamine [O-GlcNAc], O-GlcNAcase [OGA], and O-GlcNAc transferase [OGT]) in 30 cases of OSCC tissues that were surgically removed and confirmed by pathology in our hospital from January 2018 to July 2020. Meanwhile, the expression levels of O-GlcNAc, OGA, and OGT under the action of the HIF-1α inhibitor PX-478 were detected by Western blotting in the human OSCC cell line (Tca8113 line). RESULTS: ① The expression of HIF-1α and O-glycosylation-related proteins in OSCC was reported at an increased level. ② The positive expression of HIF-1α was associated with the age and tumor size of OSCC patients (P < 0.05); the positive expression of O-GlcNAc and OGT was related to the tumor size of OSCC patients (P < 0.05). ③ Expression of HIF-1α, O-GlcNAc and OGT in OSCC tissues was positively correlated (φcorrelation coefficient = 0.550). ④ Under HIF-1α inhibition, a statistically significant decrease occurred in the expression levels of O-GlcNAc and OGT at a dose of 25 µM PX-478 (P < 0.05), but a statistically significant increase occurred in OGA (P < 0.05). ⑤ Under the action of PX-478, there was a statistically significant and gradual decrease in the OGT content over time (P < 0.05). CONCLUSIONS: The expression of HIF-1α and O-glycosylation-related proteins increases in OSCC, and the expression level increases proportionally with tumor volume. Expression of HIF-1α and O-GlcNAc and OGT was positively correlated. HIF-1α inhibition by PX-478 led to decreased expression levels of O-GlcNAc and OGT but the increased expression level of OGA. PX-478 can affect Tca8113 glycosylation by reducing the expression level of OGT.

Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers.

Amomum tsao-ko Crevost & Lemarié is an important crop that has been widely used in traditional Chinese medicine and daily diets for a long time. In this study, the genetic diversity and relationships of eight cultivated populations of A. tsao-ko grown in Southwest China were examined using sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers. The results showed that 139 (99.29%) of 140 and 185 (99.46%) of 186 bands were polymorphic by SRAP and ISSR primers amplification, respectively. The polymorphic information content of detected bands were 0.270 (SRAP) and 0.232 (ISSR), respectively. The average Nei's gene diversity (H = 0.217) and Shannon's information index (I = 0.348) at the species level generated by SRAP primer were higher than those by ISSR analysis (H = 0.158, I = 0.272). Genetic differentiation coefficients and molecular variance analysis (AMOVA) indicated that the genetic variance of A. tsao-ko mainly occurred within populations rather than among populations. The high genetic identity among populations was revealed by SRAP (0.937) and ISSR (0.963). Using UPGMA cluster analysis, principal coordinate analysis, and population structure analysis, the accessions were categorized into two major groups. Overall, results obtained here will be useful for A. tsao-ko germplasm characterization, conservation, and utilization.

Development of 23 novel microsatellite markers of Amomum tsao-ko (Zingiberaceae) based on restriction-site-associated DNA sequencing.

Amomum tsao-ko (Zingiberaceae) is a traditional Chinese medicine and condiment, and an important economic crop in the tropical forest of southwest China. However, few simple sequence repeat (SSR) markers are available in A. tsao-ko, which is hindering genetic research in this species. The aim of this study was to develop and characterize microsatellite markers for A. tsao-ko using restriction-site-associated DNA sequencing. A total of 115,482 microsatellites were identified using MISA software, and 13,411 SSR primer pairs were designed. 100 pairs of SSR primers were selected at random and used to evaluate polymorphisms among 4 A. tsao-ko samples. Finally, 23 pairs of SSR primers with clear bands and obvious polymorphism were selected for genetic diversity analysis of 72 A. tsao-ko accessions. The number of alleles and effective number of alleles per locus ranged from 2 to 6 and from 1.315 to 3.776, respectively. The observed heterozygosity ranged from 0.208 to 0.779, and the expected heterozygosity was from 0.239 to 0.735. The average values of the polymorphic information content were 0.454. Hardy-Weinberg equilibrium (HWE) analysis showed that 10 loci significantly deviated from HWE (P < 0.05). The pairwise FST and genetic distance values revealed low levels of genetic differentiation and high genetic similarity among six A. tsao-ko populations. These microsatellite markers developed will provide a valuable tool for further germplasm characterization, genetic diversity, and breeding studies in A. tsao-ko.

[Effects of different water harvesting modes on alfalfa planting in semi-arid areas of Northwest China].

A field experiment with complete random design was conducted to investigate the effects of different mulching materials [common plastic film (CMR), biodegradable mulch film (BMR), and soil crust (SR)] and different ratios of furrow to ridge (60 cm:30 cm, 60 cm:45 cm, and 60 cm:60 cm) on the runoff efficiency, soil water storage, soil water content, and hay yield and water use efficiency of alfalfa in semiarid areas of the Loess Plateau. The runoff efficiency in treatments SR, BMR, and CMR was 32.0%, 90.7%, and 96.4%, respectively. In the early growth period of alfalfa (from April to June) , the soil water storage between the treatments had no significant difference, but in the late growth period (from July to September), the soil water storage in CMR and BMR was significantly higher than that in SR. The soil water storage in SR was significantly higher than that in traditional planting (TP). At budding stage, the soil water storage in TP, SR, BMR, and CMR was 223.27, 248.56, and 277. 81, and 284.16 mm, respectively. In the whole growth period, the hay yield of alfalfa in TP, SR, BMR, and CMR was 4112.1, 3397.5, 4317.8, and 4523.8 kg x hm(-2), and the water use efficiency was 11.08, 10.48, 14.56, and 14.95 kg x mm(-1) x hm(-2), respectively. The ratio of furrow to ridge had no significant effects on the water use efficiency in the same treatments. When the ratio of furrow to ridge was 60 cm:44 cm, the hay yield in CMR and BMR reached the maximum.