GWAS of grain color and tannin content in Chinese sorghum based on whole-genome sequencing.

KEY MESSAGE: Seventy-three QTL related to grain color and tannin content were identified in Chinese sorghum accessions, and a new recessive allelic variant of TAN2 gene was discovered. Sorghum is mainly used for brewing distilled liquors in China. Since grain tannins play an important role in liquor brewing, accurately understanding the relationship between grain color and tannin content can provide basis for selection standards of tannin sorghum. We resequenced a panel of 242 Chinese sorghum accessions and performed population structure and genome-wide association study (GWAS) to identify quantitative trait locus (QTL) affecting pericarp color, testa pigment, and tannin content. Phylogenetic analysis, principal component analysis (PCA), and admixture model were used to infer population structure. Two distinct genetic sub-populations were identified according to their corresponding northern and southern geographic origin. To investigate the genetic basis of natural variation in sorghum grain color, GWAS with 2,760,264 SNPs was conducted in four environments using multiple models (Blink, FarmCPU, GLM, and MLM). Seventy-three QTL were identified to be associated for the color of exocarp, mesocarp, testa, and tannin content on all chromosomes except chromosome 5, of which 47 might be novel QTL. Some important QTL were found to colocalize with orthologous genes in the flavonoid biosynthetic pathway from other plants, including orthologous of Arabidopsis (Arabidopsis thaliana) TT2, TT7, TT12, TT16 and AT5G41220 (GST), as well as orthologous of rice (Oryza sativa) MYB61 and OsbHLH025. Our investigation of the variation in grain color and tannin content in Chinese sorghum germplasm may help guide future sorghum breeding for liquor brewing.

To Explore the Safety of 3R Nursing and Dietary Nutrition Intervention in Elderly Patients with Vascular Dementia and the Effect of Improving the Self-Care Ability of Patients.

Objective: Exploring the application safety of 3R nursing and dietary nutrition intervention in elderly vascular dementia, as well as the application value of improving patients' self-care ability in elderly vascular dementia. Method: 120 elderly patients with vascular dementia in our hospital from August 2020 to June 2022 were selected as the research subjects and divided into an observation group (n = 60) and a control group (n = 60) using a random number table method. The control group received routine care+3R care, while the observation group received dietary and nutritional interventions on the basis of the control group. Compare the Mini Mental State Examination (MMSE), Neuropsychiatric Inventory Questionnaire (NPI-Q) before and after intervention between two groups, and investigate the Activities of Daily Living (ADL), Quality of Life Alzheimer's Disease (QOL-AD) Score with the Simplified Fugl Meyer Motor Function Rating Scale (FMA) and calculate nursing satisfaction. Result: After intervention, the MMSE score of the observation group was significantly higher than that of the control group, with a statistically significant difference (P < .05). The NPI-Q score was significantly lower than that of the control group, with a statistically significant difference (P < .05). After intervention, the ADL score of the observation group was significantly lower than that of the control group, with a statistically significant difference (P < .05). The QOL-AD score was significantly higher than that of the control group, with a statistically significant difference (P < .05). After intervention, the FMA score of the observation group was significantly higher than that of the control group, with a statistically significant difference (P < .05). In addition, the incidence of adverse reactions in the observation group was significantly lower than that in the control group, with a statistically significant difference (P < .05). There was no statistically significant difference in the number of people who were basically satisfied and needed improvement between the two groups (P > .05). The observation group had significantly more people who were very satisfied than the control group, and the number of people who were dissatisfied was significantly lower than the control group, with a statistically significant difference (P < .05). Conclusion: 3R nursing with diet and nutrition intervention improves safety, self-care ability, cognitive function, and nursing satisfaction in elderly patients with vascular dementia, suggesting its potential for clinical implementation.

Sorghum qTGW1a encodes a G-protein subunit and acts as a negative regulator of grain size.

Grain size is a major determinant of grain yield in sorghum and other cereals. Over 100 quantitative trait loci (QTLs) of grain size have been identified in sorghum. However, no gene underlying any grain size QTL has been cloned. Here, we describe the fine mapping and cloning of one grain size QTL. From an F8 recombinant inbred line population derived from a cross between inbred lines 654 and LTR108, we identified 44 grain size QTLs. One QTL, qTGW1a, was detected consistently on the long arm of chromosome 1 in the span of 4 years. Using the extreme recombinants from an F2:3 fine-mapping population, qTGW1a was delimited within a ~33 kb region containing three predicted genes. One of them, SORBI_3001G341700, predicted to encode a G-protein γ subunit and homologous to GS3 in rice, is likely to be the causative gene for qTGW1a. qTGW1a appears to act as a negative regulator of grain size in sorghum. The functional allele of the putatively causative gene of qTGW1a from inbred line 654 decreased grain size, plant height, and grain yield in transgenic rice. Identification of the gene underlying qTGW1a advances our understanding of the regulatory mechanisms of grain size in sorghum and provides a target to manipulate grain size through genome editing.

QTL analysis of sorghum grain traits based on high-density genetic map.

Sorghum grain traits are important agronomic traits directly related to yield and are key factors affecting the brewing process of distill liquor. Exploring the genes controlling those traits is of great significance for understanding the genetic mechanism of sorghum grain development. In this study, we conducted genotyping using Super-GBS technology on a recombinant inbred lines (RILs) population derived from the cross between "BTx623" and "Hongyingzi," consisting of 205 lines. The grain-related traits of the RIL population were investigated in Guiyang, Anshun in Guizhou, and Ledong in Hainan in China. By inclusive composite interval mapping (ICIM) method, a total of 47 quantitative trait locus (QTL) related to four grain traits (thousand grain weight, grain length, grain width, and length-width ratio) were identified across 10 chromosomes. Among them, 20 important QTL were repeatedly detected in multiple traits or environments and distributed on chromosomes 1 (1), 2 (2), 3 (5), 4 (5), 5 (1), 6 (2), 7 (2), 8 (1), and 9 (1). Six candidate genes were identified within the confidence interval of these QTL, and they are homologous to genes controlling rice grain development (OsMADS1, RGG2, OsNST1, SMG1, OsGRF8, and OsAP2-39). The results provide a basis for further cloning and functional verification of these candidate genes.

Identification of QTLs associated with tissue culture response through sequencing-based genotyping of RILs derived from 93-11 × Nipponbare in rice (Oryza sativa).

KEY MESSAGE : The performance of callus induction and callus differentiation was evaluated by 9 indices for 140 RILs; 2 major QTLs associated with plant regeneration were identified. In order to investigate the genetic mechanisms of tissue culture response, 140 recombinant inbred lines (RILs) derived from 93-11 (Oryza sativa ssp. indica) × Nipponbare (Oryza sativa ssp. japonica) and a high quality genetic map based on the SNPs generated from deep sequencing of the RIL genomes, were used to identify the quantitative trait loci (QTLs) associated with in vitro tissue culture response (TCR) from mature seed in rice. The performance of callus induction was evaluated by indices of induced-callus color (ICC), induced-callus size (ICS), induced-callus friability (ICF) and callus induction rate (CIR), respectively, and the performance of callus differentiation was evaluated by indices of callus proliferation ability (CPA), callus browning tendency (CBT), callus greening ability (CGA), the average number of regenerated shoots per callus (NRS) and regeneration rate (%, RR), respectively. A total of 25 QTLs, 2 each for ICC, ICS, ICF, CIR and CBA, 3 for CPA, 4 each for CGA, NRS and RR, respectively, were detected and located on 8 rice chromosomes. Significant correlations were observed among the traits of CGA, NRS and RR, and QTLs identified for these three indices were co-located on chromosomes 3 and 7, and the additive effects came from both Nipponbare and 93-11, respectively. The results obtained from this study provide guidance for further fine mapping and gene cloning of the major QTL of TCR and the knowledge of the genes underlying the traits investigated would be very helpful for revealing the molecular bases of tissue culture response.

Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods.

The productivity of sorghum is mainly determined by agronomically important traits. The genetic bases of these traits have historically been dissected and analysed through quantitative trait locus (QTL) mapping based on linkage maps with low-throughput molecular markers, which is one of the factors that hinder precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, an ultra-high-density linkage map based on high-quality single nucleotide polymorphisms (SNPs) generated from low-coverage sequences (~0.07 genome sequence) in a sorghum recombinant inbred line (RIL) population was constructed through new sequencing technology. This map consisted of 3418 bin markers and spanned 1591.4 cM of genome size with an average distance of 0.5 cM between adjacent bins. QTL analysis was performed and a total of 57 major QTLs were detected for eight agronomically important traits under two contrasting photoperiods. The phenotypic variation explained by individual QTLs varied from 3.40% to 33.82%. The high accuracy and quality of this map was evidenced by the finding that genes underlying two cloned QTLs, Dw3 for plant height (chromosome 7) and Ma1 for flowering time (chromosome 6), were localized to the correct genomic regions. The close associations between two genomic regions on chromosomes 6 and 7 with multiple traits suggested the existence of pleiotropy or tight linkage. Several major QTLs for heading date, plant height, numbers of nodes, stem diameter, panicle neck length, and flag leaf width were detected consistently under both photoperiods, providing useful information for understanding the genetic mechanisms of the agronomically important traits responsible for the change of photoperiod.

Selection Signatures in Chinese Sorghum Reveals Its Unique Liquor-Making Properties.

Chinese sorghum (S. bicolor) has been a historically critical ingredient for brewing famous distilled liquors ever since Yuan Dynasty (749 ∼ 652 years BP). Incomplete understanding of the population genetics and domestication history limits its broad applications, especially that the lack of genetics knowledge underlying liquor-brewing properties makes it difficult to establish scientific standards for sorghum breeding. To unravel the domestic history of Chinese sorghum, we re-sequenced 244 Chinese sorghum lines selected from 16 provinces. We found that Chinese sorghums formed three distinct genetic sub-structures, referred as the Northern, the Southern, and the Chishui groups, following an obviously geographic pattern. These sorghum accessions were further characterized in liquor brewing traits and identified selection footprints associated with liquor brewing efficiency. An importantly selective sweep region identified includes several homologous genes involving in grain size, pericarp thickness, and architecture of inflorescence. Our result also demonstrated that pericarp strength rather than grain size determines the ability of the grains to resist repeated cooking during brewing process. New insight into the traits beneficial to the liquor-brewing process provides both a better understanding on Chinese sorghum domestication and a guidance on breeding sorghum as a multiple use crop in China.

Seed size is determined by the combinations of the genes controlling different seed characteristics in rice.

Rice seed size is an important agronomic trait in determining the yield potential, and four seed size related genes (GS3, GW2, qSW5/GW5 and GIF1) have been cloned in rice so far. However, the relationship among these four genes is still unclear, which will impede the process of gene pyramiding breeding program to some extent. To shade light on the relationship of above four genes, gene expression analysis was performed with GS3-RNAi, GW2-RNAi lines and CSSL of qSW5 at the transcriptional level. The results clearly showed that qSW5 and GW2 positively regulate the expression of GS3. Meanwhile, qSW5 can be down-regulated by repression of GW2 transcription. Additionally, GIF1 expression was found to be positively regulated by qSW5 but negatively by GW2 and GS3. Moreover, the allelic effects of qSW5 and GS3 were detailedly characterized based on a natural population consisting of 180 rice cultivars. It was indicated that mutual interactions exist between the two genes, in which, qSW5 affecting seed length is masked by GS3 alleles, and GS3 affecting seed width is masked by qSW5 alleles. These findings provide more insights into the molecular mechanisms underlying seed size development in rice and are likely to be useful for improving rice grain yield.

Development of a Pedigreed Sorghum Mutant Library.

Induced mutagenesis is a powerful approach to generate variations for elucidation of gene function and to create new traits for breeding. Here, we described a procedure to develop a pedigreed mutant library through chemical mutagenesis with ethylmethane sulfonate (EMS) treated seeds in sorghum and discussed its potential to generate new traits for sorghum improvement. Unlike random mutagenesis, a pedigreed mutant library, once properly established, can serve as a powerful resource to isolate and recover mutations of both agronomical and biological importance. With the development of affordable and high-throughput next-generation sequencing technologies, identification of causal mutations from a mutant library with a uniform genetic background becomes increasingly efficient and cost-effective. Fast causal gene discovery from mutant libraries combined with precise genome editing techniques will accelerate incorporation of new traits and revolutionize crop breeding.

Molecular cloning and expression analysis of duplicated polyphenol oxidase genes reveal their functional differentiations in sorghum.

Polyphenol oxidase (PPO) is believed to play a role in plant growth, reproduction, and resistance to pathogens and pests. PPO causes browning of grains in cereals. In this study, genetic mapping of sorghum grain for phenol color reaction (PHR) was performed using a recombinant inbred line population. Only one locus was detected between SSR markers SM06072 and Xtxp176 on chromosome 6. Two linked orthologous genes (Sb06PPO1 and Sb06PPO2) within the mapped region were discovered and cloned. Transformation experiments using Nipponbare (a PHR negative rice cultivar) showed that Sb06PPO1 from LTR108 and two Sb06PPO2 alleles from both varieties could complement Nipponbare, whereas Sb06PPO1 from 654 could not. Subsequent quantitative real-time PCR (qPCR) experiments showed that Sb06PPO1 and Sb06PPO2 functioned diversely, Sb06PPO1 was mainly expressed in young panicles before flowering. Sb06PPO2 was strongly expressed in flowering panicles, especially in hulls and branches at filling stage. Moreover, the expression of Sb06PPO1 was found to be significantly up-regulated by exogenous ABA and salt, whereas Sb06PPO2 was not changed significantly, further demonstrating functional differentiation between the two genes.

Dissection of additive, epistatic effect and Q x E interaction of quantitative trait loci influencing stigma exsertion under water stress in rice.

Four flowering related traits, spikelet number per panicle (SNP), percentage of single exserted stigma (PSES), dual exserted stigma (PDES) and total exserted stigma (PES) of a RI population with 185 lines under water stress and non-stress conditions for 2 years, were investigated in a drought tolerance screening facility. ANOVA results showed high significance between years, lines, and water stress treatments, together with interactions among them in pairs. Highest phenotypic correlation was found between PSES and PES (r = 0.9752***), followed by PDES and PES (r = 0.7150***), and PSES and PDES (r = 0.5424***). Based on a linkage map of 203 SSR markers, six main effect QTLs were detected for SNP and three or four main effect QTLs were associated with PSES, PDES and PES under stress or non-stress conditions. There were one to nine pairs of epistatic QTLs influencing SNP and stigma exsertion. The contribution rates of additive and epistatic effects seemed to be in a low magnitude for most cases (0.76%-9.92%) while a few QTLs or QTL pairs explained more than 10% of total variance. Some main effect QTL and epistasis were commonly detected among PSES, PDES and PES, explaining the high positive correlation between them. Few QTLs were detected under both water stress and non-stress condition, implying that drought had severe impact on the genetic behaviors of both spikelet number and stigma exsertion.

Optimized Ultrasonic-Assisted Extraction of Polysaccharides from Chinese Traditional Medicinal Plant Paris fargesii Using Orthogonal Design.

Paris fargesii is a famous Chinese traditional medicinal plant used as antipyretic, antidotal, antiphlogistic and analgesic. This research aimed at the determination of the total polysaccharides contents in P. fargesii, which were collected from Baoxing country of Sichuan Province in order to get the optimized extraction technology. Ultrasonic method was adopted in the extraction of total polysaccharides from P. fargesii. Through single factor experiment and orthogonal test, the effects of ultrasonic extraction conditions on the total polysaccharides extraction were measured, including solid-liquid ratio, ultrasonic temperature, ultrasonic power and ultrasonic time. Then colorimetric method was applied for the assaying. The optimized extraction conditions of total polysaccharides from P. fargesii were as follows: ultrasonic power: 600w, solid-liquid ratio: 1:20, ultrasonic extraction time: 1.5h and ultrasonic temperature: 90℃. Under the optimum parameters, the total polysaccharides extraction efficiency was 0.0715%.