Genetic Analysis and Gene Mapping of a Rice Tiller Angle Mutant tac2

Tiller angle, a very essential agronomic trait, is significant in rice breeding, especially in plant type breeding. A tiller anglo controlling 2 （tac2） mutant was obtained from a restorer line Jinhui 10 by ethyl methane sulphonate mutagenesis. The tac2 mutant displayed normal phenotype at the seedling stage and the tiller angle significantly increased at the tillering stage, A preliminary physiological research indicated that the mutant was sensitive to GA. Thus, it is speculated that TAC2 and TAC1 might control the tiller angle in the same way. Genetic analysis showed that the mutant trait was controlled by a major recessive gene and was located on chromosome 9 using SSR markers. The genetic distances between TAC2 and its nearest markers RM3320 and RM201 were 19.2 cM and 16,7 cM, respectively.

Genetic Analysis and Gene Mapping of Light Brown Spotted Leaf Mutant in Rice

A light brown spotted-leaf mutant of rice was isolated from an ethane methyl sulfonate （EMS）- induced IR64 mutant bank. The mutant, designated as Ibsll （light brown spotted-leaf 1）, displayed light brown spot in the whole growth period from the first leaf to the flag leaf under natural summer field conditions. Agronomic traits including plant height, growth duration, number of filled grains per panicle, seed-setting rate and 1000-grain weight of the mutant were significantly affected. Genetic analysis showed that the mutation was controlled by a single recessive gene, tentatively named Ibsll（t）, which was mapped to the short arm of chromosome 6. By developing simple sequence repeat （SSR） markers, the gene was finally delimited to an interval of 130 kb between markers RM586 and RM588. The Ibsll（t） gene is likely a novel rice spotted-leaf gene since no other similar genes have been identified near the chromosomal region. The genetic data and recombination populations provided will facilitate further fine-mapping and cloning of the gene.

Identification and Gene Mapping of a multi-floret spikelet 1 (mfs1) Mutant Associated with Spikelet Development in Rice

In this study, a rice spikelet mutant, multi-floret spikelet 1 （mfsl）, which was derived from ethylmethane sulfonate （EMS）- treated Jinhui 10 （Oryza sativa L. ssp. indica） exhibited pleiotropic defects in spikelet development. The mfsl spikelet displayed degenerated the empty glume, elongated the rachilla, the extra lemma-like organ and degraded the palea. Additionally, mfsl flowers produced varied numbers of inner floral organs. The genetic analysis revealed that the mutational trait was controlled by a single recessive gene. With 401 recessive individuals from the F2 segregation population, the MFS1 gene was finally mapped on chromosome 5, an approximate 350 kb region. The present study will be useful for cloning and functional analysis of MFS1, which would facilitate understanding of the molecular mechanism involved in spikelet development in rice.

Identification and Gene Mapping of Completely Dominant Earliness in Rice

The completely dominant earliness was identified in a genie male-sterile and early maturing indica line 6442S-7. F1 progenies from 6442S-7 crossed with thirteen various types of medium- or late-maturing varieties, shared the same heading date as 6442S-7. The segregation of heading date in the F2 and B1F1 populations showed that the earliness of 6442S-7 is mainly controlled by two dominant major genes. The local linkage map of one dominant earliness gene harbored in 6442S-7 was constructed with F2 population and four kinds of molecular marker techniques. The results showed that the gene was located between a RFLP marker C515 and a RAPD marker OPI 11.557 on the terminal region of short arm of rice chromosome 3, 10.9cM and 1.5cM from C515 and OPI11.557, respectively. The genetic distances from the target gene to two SSR markers, RM22 and RM231, and one AFLP marker, PT671, were 3.0, 6.7 and 12.4 cM, respectively. This gene, being identified and mapped first, is designated tentatively as Ef-cd(t). As a new genetic resource of completely dominant earliness, 6442S-7 has splendid future in rice improvement.

Identification and gene mapping of the starch accumulation and premature leaf senescence mutant ossac4 in rice

The rice mutant ossac4(starch accumulating 4)was raised from seeds of the rice(Oryza sativa L.)indica maintainer line Xinong 1B treated with ethyl methanesulfonate.The distal and medial portions of the second leaf displayed premature senescence in the ossac4 mutant at the four-leaf stage.Physiological and biochemical analysis,and cytological examination revealed that the ossac4 mutant exhibited the premature leaf senescence phenotype.At the four-leaf stage,the leaves of the ossac4 mutant exhibited significantly increased contents of starch compared with those of the wild type(WT).Quantitative real-time PCR analysis showed that the expression levels of photosynthesis-associated genes were down-regulated and the expression levels of glucose metabolism-associated genes were abnormal.Genetic analysis indicated that the ossac4 mutation was controlled by a single recessive nuclear gene.The OsSAC4 gene was localized to a 322.7-kb interval between the simple-sequence repeat marker XYH11-90 and the single-nucleotide polymorphism marker SNP5300 on chromosome 11.The target interval contained 20 annotated genes.The present results demonstrated that ossac4 represents a novel starch accumulation and premature leaf senescence mutant,and lays the foundation for cloning and functional analysis of OsSAC4.

Gene Mapping of Brachytic Stem and Its Effect on Main Agronomic Traits in Soybean

Brachytic stem is a major trait in plant type .of soybean and its yield potential may be higher under high population when compared with normal stem. In the present investigation, 152 recombinant inbred line （RIL） families derived from the cross of Bogao （normal stem） and Nannong 94-156 （brachytic stem） were used to map genes and QTLs of three plant type traits and to identify the effects of brachytic stem on agronomic traits such as yield. The primary results indicated that brachytic stem （sb） and determinate growth habit （drl） were mapped on linkage groups B2 and L, three major QTLs related to plant height were detected and mapped on linkage group L near drl, another minor QTL was mapped near sb on linkage group B2-1. Lines with brachytic stem had shorter plant height, lower biomass, yield, harvest index and pods per plant, and essentially no differences in days to maturity and 100-seed weight when compared with normal stem lines. It was obvious that the effect of brachytic stem on yield was due to the decreased height, biomass and harvest index.

Heredity and gene mapping of a novel white stripe leaf mutant in wheat

Spotted leaf(spl)mutant is a type of leaf lesion mimic mutants in plants.We obtained some lesion mimic mutants from ethyl methane sulfonate(EMS)-mutagenized wheat(Triticum aestivum L.)cultivar Guomai 301(wild type,WT),and one of them was named as white stripe leaf(wsl)mutant because of the white stripes on its leaves.Here we report the heredity and gene mapping of this novel wheat mutant wsl.There are many small scattered white stripes on the leaves of wsl throughout its whole growth period.As the plants grew,the white stripes became more severe and the necrotic area expanded.The mutant wsl grew only weakly before the jointing stage and gradually recovered after jointing.The length and width of the flag leaf,spike number per plant and thousand-grain weight of wsl were significantly lower than those of the WT.Genetic analysis indicated that the trait of white stripe leaf was controlled by a recessive gene locus,named as wsl,which was mapped on the short arm of chromosome 6 B by SSR marker assay.Four SSR markers in the F2 population of wsl×CS were linked to wsl in the order of Xgpw1079–Xwmc104–Xgwm508-wsl–Xgpw7651 at 7.1,5.2,8.7,and 4.4 c M,respectively and three SSR markers in the F2 population of wsl×Jimai 22 were linked to wsl in the order of Xgwm508–Xwmc494–Xgwm518-wsl at 3.5,1.6 and 8.2 c M,respectively.In comparison to the reference genome sequence of Chinese Spring(CS),wsl is located in a 91-Mb region from 88 Mb(Xgwm518)to 179 Mb(Xgpw7651)on chromosome 6 BS.Mutant wsl is a novel germplasm for studying the molecular mechanism of wheat leaf development.

Genetic Analysis and Gene Mapping of Short Root Mutant Rice ksr1

A short root mutant ksrl with the Kasalath background was isolated from an EMS-mutagenized population in rice. The root length of 6-day-old ksr1 seedlings was only about 20% of the wild type. Genetic analysis indicated that the short root phenotype of ksrl was controlled by a recessive mutation in a single nuclear-encoded gene. To map the ksrl mutation, an F2 population was generated by crossing the ksrl mutant with Nipponbare. The KSR1 locus was linked to the SSR marker RM1223 on rice chromosome 4. Eight new SSR markers and two InDel markers were developed around this marker. KSR1 gene was further mapped to a 155 kb region, flanked by the InDel marker 4-24725K and the SSR marker RM17182.

Genetic Analysis and Gene Mapping of Multi-tiller and Dwarf Mutant d63 in Rice

A spontaneous mutation, tentatively named d63, was derived from the twin-seedling progenies of rice crossed by diploid SARIII and Minghui 63. Compared with wild-type plants, the d63 mutant showed multiple abnormal phenotypes, such as dwarfism, more tillers, smaller flag leaf and reduced seed-setting rate and 1000-grain weight. In this study, two F2 populations were developed by crossing between d63 and Nipponbare, d63 and 93-11. Genetic analysis indicated that d63 was controlled by a single recessive gene, which was located on the short arm of chromosome 8, within the genetic distance of 0.40 cM from RM22195. Hence, D63 might be a new gene as there are no dwarf genes reported on the short arm of chromosome 8.

Gene mapping and candidate gene analysis of multi-floret spikelet 3(mfs3) in rice(Oryza sativa L.)

Rice(Oryza sativa L.) is one of the most important food crops worldwide and a model monocot plant for gene function analysis, so it is an ideal system for studying flower development. This study reports a mutant, named multi-floret spikelet 3(mfs3), which is related to the spikelet development in rice and derived from the ethylmethane sulfonate(EMS)-treated rice cultivar XIDA 1 B. In mfs3, the main body of palea(bop) was degenerated severely and only glume-like marginal regions of palea(mrp) remained, while other floral organs developed normally, indicating that the palea identity was seriously influenced by the mutation. It was also observed that the number of floral organs was increased in some spikelets, including 2 lemmas, 4 mrp, 4 lodicules, 8–10 stamens, and 2 pistils, which meant that the spikelet determinacy was lost to some degree in mfs3. Furthermore, genetic analysis demonstrated that the mfs3 trait was controlled by a single recessive gene. Using 426 F2 mutants derived from the cross between sterile line 56 S and mfs3, the MULTI-FLORET SPIKELET 3(MFS3) gene was mapped between the molecular markers RM19347 and RM19352 on Chr.6, with a physical distance of 106.3 kb. Sequencing of candidate genes revealed that an 83-bp fragment loss and a base substitution occurred in the LOC_Os06 g04540 gene in the mutant, confirming preliminarily that the LOC_Os06 g04540 gene was the MFS3 candidate gene. Subsequent q PCR analysis showed that the mutation caused the down-regulation of Os MADS1 and FON1 genes, and the up-regulation of Os IDS1 and SNB genes, which are all involved in the regulation of spikelet development. The MFS3 mutation also significantly reduced the transcription of the REP gene, which is involved in palea development. These results indicated that the MFS3 gene might be involved in the spikelet meristem determinacy and palea identity by regulating the expression of these related genes.

Gene mapping and candidate gene analysis of aberrant-floral spikelet 1(afs1) in rice(Oryza sativa L.)

The spikelet is a unique inflorescence structure in grasses. However, the molecular mechanism that regulates its development remains unclear, and we therefore characterize a spikelet mutant of rice(Oryza sativa L.), aberrant-floral spikelet 1(afs1), which was derived from treatment of Xinong 1 B with ethyl methanesulfonate. In the afs1 mutant, the spikelet developed an additional lemma-like organ alongside the other normally developed floral organs, and the paleae were degenerated to differing degrees with or without normally developed inner floral organs. Genetic analysis revealed that the afs1 phenotype was controlled by a single recessive gene. The AFS1 gene was mapped between the insertion/deletion(In Del) marker Indel19 and the simple sequence repeat marker RM16893, with a physical distance of 128.5 kb on chromosome 4. Using sequence analysis, we identified the deletion of a 5-bp fragment and a transversion from G to A within LOC_Os04 g32510/LAX2, which caused early termination of translation in the afs1 mutant. These findings suggest that AFS1 may be a new allele of LAX2, and is involved in the development of floral organs by regulating the expression of genes related to their development. The above results provide a new view on the function of LAX2, which may also regulate the development of spikelets.

Utilization of Gene Mapping and Candidate Gene Mutation Screening for Diagnosing Clinically Equivocal Conditions: A Norrie Disease Case Study

Prenatal diagnosis was requested for an undiagnosed eye disease showing X-linked inheritance in a family. No medical records existed for the affected family members..Mapping of the X chromosome and candidate gene mutation screening identified a c.C267A[p.F89L] mutation in NPD previously described as possibly causing Norrie disease..The detection of the c.C267A[p.F89L] variant in another unrelated family confirms the pathogenic nature of the mutation for the Norrie disease phenotype. Gene mapping, haplotype analysis, and candidate gene screening have been previously utilized in research applications but were applied here in a diagnostic setting due to the scarcity of available clinical information..The clinical diagnosis and mutation identification were critical for providing proper genetic counseling and prenatal diagnosis for this family.

Design Process Optimization Based on Design Process Gene Mapping

The idea of genetic engineering is introduced into the area of product design to improve the design efficiency. A method towards design process optimization based on the design process gene is proposed through analyzing the correlation between the design process gene and characteristics of the design process. The concept of the design process gene is analyzed and categorized into five categories that are the task specification gene, the concept design gene, the overall design gene, the detailed design gene and the processing design gene in the light of five design phases. The elements and their interactions involved in each kind of design process gene signprocess gene mapping is drawn with its structure disclosed based on its function that process gene.

Mapping of Purple Gene in Spears of Asparagus(Asparagus officinalis L.)

[Objectives]This study was conducted to find out regulatory genes related to purple in spears of asparagus(Asparagus officinalis L.).[Methods]The stable asparagus inbred line JX1513-5(the base of the spear is purple)and JLV1718-7(the base of the spear is green)were used as parents to study the genetic law of purple/green traits in their offspring.[Results]The results showed that the purple in the basal part of asparagus spear was controlled by a pair of alleles,and purple was dominant over green.The F 2 segregation population was resequenced by the bulk segregation analysis(BSA)method,and the purple trait in the basal part of asparagus spear was located in the interval of 24.51-25.08 Mb on Chr07 chromosome,which included 47 genes.According to the annotation information,three candidate genes were screened out:LOC109849403,LOC109849430 and LOC109849442.The candidate genes were verified by real-time fluorescence quantitative PCR(qRT-PCR),and finally LOC109849442 was obtained as the candidate gene for controlling the purple/green trait in the basal part of asparagus spear.[Conclusions]This study lays a foundation for the breeding of new asparagus varieties and molecular marker-assisted breeding.

Identification and fine mapping of a fertility restorer gene for wild abortive cytoplasmic male sterility in the elite indica rice non-restorer line 9311

The wild abortive(WA)-type cytoplasmic male sterility(CMS)derived from the wild rice species Oryza rufipogon Griff.is used widely in three-line indica hybrids.The identification and mapping of restorer of fertility(Rf)genes aided in the development of WA-type hybrids.Here we report that testcross F1 plants from the WA-type CMS line and 9311 exhibited stainable pollen grains with no seed set,indicating that 9311 carries minor-effect Rfs for WA-type CMS.We developed an advanced backcross population consisting of plants harboring small regions of donor chromosomal segments from 9311 in the WATianfeng A genetic background with moderate seed setting rates.Genetic analysis showed that the pollen fertility levels of the backcross individuals are governed by a single gene from 9311 that we named Rf19(t).By use of the RICE 40 K gene chip,three introduced segments were identified in the fertile lines,and a candidate region spanning 4.37–8.29 Mb on chromosome 1 was identified for Rf19(t).Finally,Rf19(t)was fine-mapped to a region of 90 kb between the DNA marker loci STS1-163 and STS1-183,in which eight ORFs were predicted.Also,using relative expression analyses,comparative sequence analyses and functional domain analyses,we identified LOC_Os01g10530 as the most likely candidate gene for Rf19(t).Furthermore,Rf19(t)was found to function in fertility restoration,most probably by regulating the degradation of m RNA transcribed from the mitochondrial gene WA352.These results increase our knowledge of fertility restoration in WA-type CMS lines and will facilitate the development of high-quality pairs of WAtype CMS and maintainer lines.

The gene encoding flavonol synthase contributes to lesion mimic in wheat

Lesion mimic often exhibits leaf disease-like symptoms even in the absence of pathogen infection,and is characterized by a hypersensitive-response(HR)that closely linked to plant disease resistance.Despite this,only a few lesion mimic genes have been identified in wheat.In this investigation,a lesion mimic wheat mutant named je0297 was discovered,showing no alteration in yield components when compared to the wild type(WT).Segregation ratio analysis of the F_(2)individuals resulting from the cross between the WT and the mutant revealed that the lesion mimic was governed by a single recessive gene in je0297.Using Bulked segregant analysis(BSA)and exome capture sequencing,we mapped the lesion mimic gene designated as lm6 to chromosome 6BL.Further gene fine mapping using 3315 F_(2)individuals delimited the lm6 within a 1.18 Mb region.Within this region,we identified 16 high-confidence genes,with only two displaying mutations in je0297.Notably,one of the two genes,responsible for encoding flavonol synthase,exhibited altered expression levels.Subsequent phenotype analysis of TILLING mutants confirmed that the gene encoding flavonol synthase was indeed the causal gene for lm6.Transcriptome sequencing analysis revealed that the DEGs between the WT and mutant were significantly enriched in KEGG pathways related to flavonoid biosynthesis,including flavone and flavonol biosynthesis,isoflavonoid biosynthesis,and flavonoid biosynthesis pathways.Furthermore,more than 30 pathogen infection-related(PR)genes exhibited upregulation in the mutant.Corresponding to this expression pattern,the flavonoid content in je0297 showed a significant decrease in the 4^(th)leaf,accompanied by a notable accumulation of reactive oxygen,which likely contributed to the development of lesion mimic in the mutant.This investigation enhances our comprehension of cell death signaling pathways and provides a valuable gene resource for the breeding of disease-resistant wheat.

Quantitative trait loci identification reveals zinc finger protein CONSTANS-LIKE 4 as the key candidate gene of stigma color in watermelon(Citrullus lanatus)

Stigma color is a critical agronomic trait in watermelon that plays an important role in pollination.However,there are few reports on the regulation of stigma color in watermelon.In this study,a genetic analysis of the F2 population derived from ZXG1553(P1,with orange stigma)and W1-17(P2,with yellow stigma)indicated that stigma color is a quantitative trait and the orange stigma is recessive compared with the yellow stigma.Bulk segregant analysis sequencing(BSA-seq)revealed a 3.75 Mb segment on chromosome 6 that is related to stigma color.Also,a major stable effective QTL Clqsc6.1(QTL stigma color)was detected in two years between cleaved amplified polymorphic sequencing(CAPS)markers Chr06_8338913 and Chr06_9344593 spanning a~1.01 Mb interval that harbors 51 annotated genes.Cla97C06G117020(annotated as zinc finger protein CONSTANS-LIKE 4)was identified as the best candidate gene for the stigma color trait through RNA-seq,quantitative real-time PCR(qRT-PCR),and gene structure alignment analysis among the natural watermelon panel.The expression level of Cla97C06G117020 in the orange stigma accession was lower than in the yellow stigma accessions with a significant difference.A nonsynonymous SNP site of the Cla97C06G117020 coding region that causes amino acid variation was related to the stigma color variation among nine watermelon accessions according to their re-sequencing data.Stigma color formation is often related to carotenoids,and we also found that the expression trend of ClCHYB(annotated asβ-carotene hydroxylase)in the carotenoid metabolic pathway was consistent with Cla97C06G117020,and it was expressed in low amounts in the orange stigma accession.These data indicated that Cla97C06G117020 and ClCHYB may interact to form the stigma color.This study provides a theoretical basis for gene fine mapping and mechanisms for the regulation of stigma color in watermelon.

MapGene2Chrom基于Perl和SVG语言绘制基因物理图谱

遗传图谱表现形式简洁明了,为分析遗传规律、克隆基因提供了便利。Gbrowse、MapViewer等工具虽然能够协助研究人员绘制相似形式的物理图谱,但有很大的局限性:(1)数据需提前布置好;(2)输出结果无法灵活修改。鉴于此,文章基于Perl和SVG语言,开发了一款生物辅助作图软件MapGene2Chrom的本地版与网页版,该软件能够依据输入数据快速绘制相应的物理图谱。该软件输入数据格式简单,输出结果易于修改,图片格式为SVG矢量图,具有很好的移植性,以期为研究人员绘制物理图谱提供便利。

Inheritance and Gene Mapping of Resistance to Soybean Mosaic Virus Strain SC14 in Soybean

Soybean mosaic virus （SMV） is one of the most broadly distributed diseases worldwide. It causes severe yield loss and seed quality deficiency in soybean （Glycine max （L.） Merr.）. SMV Strain SC14 isolated from Shanxi Province, China, was a newly identified virulent strain and can infect Kefeng No. 1, a source with wide spectrum resistance. In the present study, soybean accessions, PI96983, Qihuang No. 1 and Qihuang No. 22 were identified to be resistant （R） and Nannong 1138-2, Pixianchadou susceptible （S） to SC14. Segregation analysis of PI96983 x Nannong 1138-2 indicated that a single dominant gene （designated as Rsc14） controlled the resistance to SC14 at both V2 and R1 developmental stages. The same results were obtained for the crosses of Qihuang No. 1 × Nannong 1138-2 and Qihuang No. 22 x Nannong 1138-2 as in PI96983 x×Nannong 1138-2 at V2 stage, but at R1 stage, the F1 performed as necrosis （a susceptible symptom other than mosaic）, F2 segregated in a ratio of 1R：2N：IS, and the progenies of necrotic （N） F2 individuals segregated also in R, N and S. It indicated that a single gene （designated as Rsc140, to be different from that of PI96983） controlled the resistance to SC14, its dominance was the same as in PI96983 × Nannong 1138-2 （without symptoms） at V2 stage and not the same at R1 stage. The tightly linked co-dominant simple sequence repeat （SSR） marker Satt334 indicated that all the heterozygous bands were completely corresponding to the necrotic F2 individuals, or all the necrotic F2 individuals were heterozygotes. It was inferred that necrosis might be due to the interaction among SMV strains, resistance genes, genetic background of the resistance genes, and plant development stage. Furthermore, the bulked segregant analysis （BSA） of SSR markers was conducted to map the resistance genes. In F2 of PI96983 × Nannong 1138-2, five SSR markers, Sat_297, Sat_234, Sat_154, Sct_033 and Sat_120, were found closely linked to Rsc14, with genetic distances of 14.5 cM, 11.3 cM, 4.3 cM, 3.2 cM and 6 cM, respectively. In F2 of Qihuang No. 1 × Nannong 1138-2,three SSR markers, Sat_234, Satt334 and Sct_033, tightly linked to Rsc140 with genetic distances of 7.2 cM, 1.4 cM and 2.8 cM, respectively. Based on the integrated joint map by Cregan et al. （1999）, both Rsc14 and Rsc140 were located between Sat_234 and Sct_033 on linkage with group F of soybean, with their distances from Sct_033 at the same side being 3.2 cM and 2.8 cM, respectively. Therefore, Rsc14 and Rsc140 might be on a same locus. The obtained information provides a basic knowledge for marker-assisted selection of the resistance gene in soybean breeding programs and fine mapping and map-based cloning of the resistance gene.

Construction of an integrated map and location of a bruchid resistance gene in mung bean

Bruchid beetle(Callosobruchus chinensis) poses a serious threat to the production and storage of mung bean(Vigna radiata). Mapping bruchid resistance(Br) will provide an important basis for cloning the responsible gene(s) and elucidating its functional mechanism, and will also facilitate marker-assisted selection in mung bean breeding. Here, we report the construction of the genetic linkage groups of mung bean and mapping of the Br1 locus using an RIL population derived from a cross between Berken, a bruchid-susceptible line, and ACC41, a bruchid-resistant line. A total of 560 markers were mapped onto 11 linkage groups,with 38.0% of the markers showing distorted segregation. The lengths of the linkage groups ranged from 45.2 to 117.0 c M with a total coverage of 732.9 c M and an average interval of1.3 c M between loci. Br1 was located on LG9 between BM202(0.7 c M) and Vr2-627(1.7 c M).Based on 270 shared SSR markers, most of the linkage groups were assigned to specific chromosomes. These results should further accelerate the genetic study of this crop.