Genome-wide association mapping for root cone angle in rice

Background

Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years.

Results

To find other QTLs linked to root cone angle, a genome-wide association mapping study was conducted on two panels of 162 indica and 169 japonica rice accessions genotyped with two sets of SNP markers (genotyping-by-sequencing set with approximately 16,000 markers and high-density-rice-array set with approximately 300,000 markers). The root cone angle of all accessions was measured using a screen protractor on images taken after 1 month of plant growth in the Rhizoscope phenotyping system. The distribution of the root cone angle in the indica panel was Gaussian, but several accessions of the japonica panel (all the bulus from Indonesia and three temperate japonicas from Nepal or India) appeared as outliers with a very wide root cone angle. The data were submitted to association mapping using a mixed model with control of structure and kinship. A total of 15 QTLs for the indica panel and 40 QTLs for the japonica panel were detected. Genes underlying these QTLs (+/?50 kb from the significant markers) were analyzed. We focused our analysis on auxin-related genes, kinases, and genes involved in root developmental processes and identified 8 particularly interesting genes.

Conclusions

The present study identifies new sources of wide root cone angle in rice, proposes ways to bypass some drawbacks of association mapping to further understand the genetics of the trait and identifies candidate genes deserving further investigation.

     

Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection

Background

Cadmium (Cd) accumulation in rice followed by transfer to the food chain causes severe health problems in humans. Breeding of low Cd accumulation varieties is one of the most economical ways to solve the problem. However, information on the identity of rice germplasm with low Cd accumulation is limited, particularly in indica, and the genetic basis of Cd accumulation in rice is not well understood.

Results

Screening of 312 diverse rice accessions revealed that the grain Cd concentrations of these rice accessions ranged from 0.12 to 1.23?mg/kg, with 24 accessions less than 0.20?mg/kg. Three of the 24 accessions belong to indica. Japonica accumulated significantly less Cd than indica (p < 0.001), while tropical japonica accumulated significantly less Cd than temperate japonica (p < 0.01). GWAS in all accessions identified 14 QTLs for Cd accumulation, with 7 identified in indica and 7 identified in japonica subpopulations. No common QTL was identified between indica and japonica. The previously identified genes (OsHMA3, OsNRAMP1, and OsNRAMP5) from japonica were colocalized with QTLs identified in japonica instead of indica. Expression analysis of OsNRAMP2, the candidate gene of the novel QTL (qCd3–2) identified in the present study, demonstrated that OsNRAMP2 was mainly induced in the shoots of high Cd accumulation accessions after Cd treatment. Four amino acid differences were found in the open reading frame of OsNRAMP2 between high and low Cd accumulation accessions. The allele from low Cd accumulation accessions significantly increased the Cd sensitivity and accumulation in yeast. Subcellular localization analysis demonstrated OsNRAMP2 expressed in the tonoplast of rice protoplast.

Conclusion

The results suggest that grain Cd concentrations are significantly different among subgroups, with Cd concentrations decreasing from indica to temperate japonica to tropical japonica. However, considerable variations exist within subgroups. The fact that no common QTL was identified between indica and japonica implies that there is a different genetic basis for determining Cd accumulation between indica and japonica, or that some QTLs for Cd accumulation in rice are subspecies-specific. Through further integrated analysis, it is speculated that OsNRAMP2 could be a novel functional gene associated with Cd accumulation in rice.

     

Genome-wide identification of TPS genes in sesame and analysis of their expression in response to abiotic stresses

Trehalose and its precursor, trehalose-6-phosphate, play critical roles in plant metabolism and response to abiotic stresses. Trehalose-6-phosphate synthase(TPS) is a key enzyme in the trehalose synthesis pathway. Hence this study identified TPS genes in sesame(Si TPSs) and examined their expression patterns under various abiotic stresses. Totally, ten Si TPSs were identified and comprehensively characterized. Si TPSs were found to be unevenly distributed on five out of 13 sesame chromosomes and...     

Research progress in rice gametophyte genes

Gametophyte genes (ga) for segregation distortion have been reported by many researchers. Iwata et al(1964) reported the presence of a gametophyte gene ga 1 on chromosome 6 which controlled a selective fertilization of gametes in the cross between an atomic-bomb-irradiated mutant and a normal variety. Nakagahra et al(1972) and Nakagahra (1972) reported two gametophyte genes ga 2 and ga 3 near the loci of marker genes bc 1 and dl on chromosome 3. When Japanese testers were crossed with some foreign varieties from Asia, the presence of ga 2 resulted in an increase ofjaponica allele while ga 3 did theopposite effect.     

Research progress in rice gametophyte genes

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Identification of cassava root protein genes

The protein population of cassava root layers was characterized bySDS-PAGE and bidimensional polyacrylamide gel electrophoresis. SDS-Pagerevealed the presence of a protein population in the molecular weight rangebetween 94 and 20 kDa. The expression pattern of these proteins was welldefined within the different layers. Partial protein sequence analyses andpreliminary results on the layer-specific expression pattern obtained withNorthern analyses are presented.     

Conditional genes for grain yield in rice

Grain yield in cereal crops was an etemal theme.     

Conditional genes for grain yield in rice

Grain yield in cereal crops was an etemal theme.     

大豆TPS基因家族全基因组鉴定、分类与表达分析

本研究利用大豆基因组数据库,通过生物信息学分析,鉴定并获得大豆TPS 家族基因所有成员的全序列、基因结构和定位信息。研究还利用序列比对对大豆TPS 家族基因进行进化和分类分析,同时通过soybase大豆发育表达芯片数据库相关信息,对该家族基因成员的组织表达谱进行了检测。研究结果表明,大豆基因组中含有20个TPS家族基因成员。系统发育分析将这些TPS基因分成了两个亚家族。基因定位分析表明,这些成员基因分别分布于大豆的14条染色体上。启动子分析表明,全部大豆TPS 家族基因的启动子区都含有逆境反应顺式作用元件。转录水平芯片数据分析同时显示,大豆TPS家族基因大多在花、根、根瘤等组织中存在优势表达。该研究结果将促进大豆TPS家族基因的功能研究与利用。     

Overexpression of potassium channel genes in rice plant

China′ s potassium fertilizer mainly depends on import and the utilization efficiency of K fertilizer was only 30% . So it is very important to enhance utilization efficiency and to reduce its applying amount by improving nutrition characteristics of plant with bioengineering techinques. Potassium channel genes AKT1 and KAT1 were the genes involved in K+ uptake. To investigate the role of heterogeneous K channel genes in the enhancement of K absorbing, genes AKT1 and KAT1 were transferred into four rice varieties, i.e. Zhonghua 8, Zhonghua 9, Zhonghua 13, and 8706.     

Physiological superiority of root system of inter-subspecific hybrid rice

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Physiological superiority of root system of inter-subspecific hybrid rice

Physiology of root system, especially root system activity,is a very important physiological trait of rice, which directly affects rice growth and development of the aerial parts and yield. Inter-subspecific hybrid rice IIyou 2070and Ilyou 419, as well as their restorer lines 2070 and Zhong419, were used to study physiological traits of rice root system. Three years research indicated that in ter-subspecific hybrid rice had root systems of physiological superiority. Results were briefly showed as the follows:     

Root response to aerobic conditions in rice,estimated by Comair root length scanner and scanner-based image analysis

Precise evaluation of root system architecture is important for understanding how rice plants are adapted to non-puddled and non-flooded conditions in aerobic culture. The objective of this study was to compare estimates of root length by the Comair root length scanner and a flat bed scanner and image analysis software in rice grown in aerobic, near-saturated and flooded fields. Fine roots (diameter < 0.2 mm) accounted for >80% of root length in all hydrological conditions. The Comair root length scanner detected fewer fine roots than the software; root length estimated by the Comair scanner was between that of roots wider than 0.1 mm and roots wider than 0.2 mm estimated by image analysis software. Importantly, total root length under aerobic and near-saturated conditions was 10–30% of that under flooding by image analysis software, but not by the Comair scanner. Digital image analysis detected genotypic differences in fine root development in the subsurface layer in aerobic culture that the Comair root length scanner would have missed. Although root length measurement by image analysis software is still under development, this new tool will facilitate the phenotyping of root system architecture and shed light on the roles of fine roots in water-saving rice cultivation.     

Development of herbicide resistance genes and their application in rice

Rice is one of the most important food crops in the world.Weeds seriously affect the rice yield and grain quality.In recent years,there are tremendous progresses in the research and application of herbicideresistant genes in rice worldwide.This article reviews the working mechanisms of six herbicides(glyphosate,glufosinate,acetolactate synthase inhibitor herbicides,acetyl-Co A carboxylase inhibitor herbicides,hydroxyhenylpyruvate dioxygenase(HPPD)inhibitor herbicides and dinitroaniline herbicides),the resistance mutations of the corresponding herbicide-target genes,and the herbicide detoxification mechanisms by non-target genes.Examples are provided on herbicide-resistant rice materials obtained by transformation of exogenous resistance genes,by artificial mutagenesis and mutant screening,and by modifying the target genes through gene editing.This paper also introduces the current application of herbicide-resistant rice,points out problems that may be caused by utilization of herbicide resistant rice and solutions to the problems,and discusses the future prospects for the development of herbicideresistant rice.     

Genome duplication improves rice root resistance to salt stress

Background

Salinity is a stressful environmental factor that limits the productivity of crop plants, and roots form the major interface between plants and various abiotic stresses. Rice is a salt-sensitive crop and its polyploid shows advantages in terms of stress resistance. The objective of this study was to investigate the effects of genome duplication on rice root resistance to salt stress.

Results

Both diploid rice (HN2026-2x and Nipponbare-2x) and their corresponding tetraploid rice (HN2026-4x and Nipponbare-4x) were cultured in half-strength Murashige and Skoog medium with 150 mM NaCl for 3 and 5 days. Accumulations of proline, soluble sugar, malondialdehyde (MDA), Na⁺ content, H⁺ (proton) flux at root tips, and the microstructure and ultrastructure in rice roots were examined. We found that tetraploid rice showed less root growth inhibition, accumulated higher proline content and lower MDA content, and exhibited a higher frequency of normal epidermal cells than diploid rice. In addition, a protective gap appeared between the cortex and pericycle cells in tetraploid rice. Next, ultrastructural analysis showed that genome duplication improved membrane, organelle, and nuclei stability. Furthermore, Na⁺ in tetraploid rice roots significantly decreased while root tip H⁺ efflux in tetraploid rice significantly increased.

Conclusions

Our results suggest that genome duplication improves root resistance to salt stress, and that enhanced proton transport to the root surface may play a role in reducing Na⁺ entrance into the roots.     

A quick determination of root resistance to water transport in paddy rice

Hydraulic resistance in plants is one of the most important factors responsible for changes in leaf water potential that is an indicator of plant water stress. Although the hydraulic resistance to passive water transport (R_pa) is a robust index in paddy rice (Oryza sativa), measurement is both time-consuming and labour-intensive. Here, we describe on a quick method to measure hydraulic resistance to osmotic water transport (R_os) by measuring the xylem sap exudation rate and osmotic water potential. In a greenhouse experiment, R_os responded significantly to soil temperature, but under field conditions soil temperature varied considerably less than air temperature. In the field experiment, R_os of six rice cultivars at two growth stages was strongly positively correlated with R_pa. We conclude that measuring R_os could be used to evaluate root water transport capacity in paddy rice under conditions with adequate soil water.     

大豆资源抗疫霉根腐病基因分析

采取下胚轴创伤接种法鉴定156份大豆资源对13个不同毒力基因型大豆疫霉菌株的抗性。结果表明,125份资源分别抗1-13个菌株,占鉴定资源总数的80.13%。125份抗性大豆资源对13个大豆疫霉菌株共产生90种反应型。通过与13个鉴别寄主的反应型比较发现,有9份大豆资源产生的5种反应型与含有已知抗病基因的大豆资源的反应型相同;12份大豆资源产生的5种反应型与已知2个抗病基因组合的反应型一致,另外,还有至少抗1个菌株的104份大豆资源产生的80种反应型,既不同于已知单个抗病基因的反应型,也不同于2个已知抗病基因组合的反应型,推测可能含有新的抗病基因或基因组合。