Flowering Date1, a major photoperiod sensitivity gene in adzuki bean,is a soybean floral repressor E1 ortholog

Adzuki bean is an important legume crop originating in temperate regions, with photoperiod in sensitivity being a key factor in its latitudinal adaptation. The Flowering Date1 (FD1) gene has a large effect on the photoperiodic response of flowering time, but the molecular basis for the effect of this locus is undetermined. The present study delimited the FD1 locus to a 17.1 kb sequence, containing a single gene, an E1 ortholog (VaE1). A comparison between Vigna angularis ‘Shumari’ (photoperiod insensitive) and ‘Acc2265’ (photoperiod sensitive) identified 29 insertions/deletions and 178 SNPs upstream of VaE1 in the FD1 locus. VaE1 expression in ‘Acc2265’ was greater under long-day than short-day conditions, whereas VaE1 expression in ‘Shumari’ was lower regardless of day length. These findings suggested that responsible gene of FD1 is a VaE1, which acts as a floral repressor by being upregulated in response to long-day conditions. The inability to upregulate VaE1 under long-day conditions was linked to its ability to flower under these conditions. These results provide greater understanding of the molecular control of a flowering date and clues enabling the breeding of adzuki bean at higher latitudes.     

Mapping of QTLs controlling epicotyl length in adzuki bean (Vigna angularis)

Epicotyl length (ECL) of adzuki bean (Vigna angularis) affects the efficiency of mechanized weeding and harvest. The present study investigated the genetic factors controlling ECL. An F₂ population derived from a cross between the breeding line ‘Tokei1121’ (T1121, long epicotyls) and the cultivar ‘Erimo167’ (common epicotyls) was phenotyped for ECL and genotyped using simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP) markers. A molecular linkage map was generated and fifty-two segregating markers, including 27 SSRs and 25 SNPs, were located on seven linkage groups (LGs) at a LOD threshold value of 3.0. Four quantitative trait loci (QTLs) for ECL, with LOD scores of 4.0, 3.4, 4.8 and 6.4, were identified on LGs 2, 4, 7 and 10, respectively; together, these four QTLs accounted for 49.3% of the phenotypic variance. The segregation patterns observed in F₅ residual heterozygous lines at qECL10 revealed that a single recessive gene derived from T1121 contributed to the longer ECL phenotype. Using five insertion and deletion markers, this gene was fine mapped to a ~255 kb region near the end of LG10. These findings will facilitate marker-assisted selection for breeding in the adzuki bean and contribute to an understanding of the mechanisms associated with epicotyl elongation.     

Effects of photoperiod and temperature on flowering in mungbean (Vigna radiata (L.) Wilczek)

Summary Forty strains of mungbeans, including all of the entries in the 1st and 2nd International Mungbean Nurseries (IMN), were grown in plant growth chambers in photoperiods of 12, 13, 14, 15, and 16 hours and mean temperatures of 18, 23, and 28°C. Results show that (1) mungbean strains differ in their flowering response to photoperiod and to mean temperature; (2) increasing the photoperiod of reducing the mean temperature delayed flowering, the amount of delay varied with the strain: (3) variations in mean temperature may alter the effect of the photoperiod on flowering in particular strains. Twenty-five strains which flowered in all photoperiod-temperature treatments could be divided into four groups, each group being successively later in flowering. The remaining 15 strains could be divided into four groups, according to their failure to flower within 105 days in specific photoperiod-temperature treatments. Flowering response in the growth chamber is useful in explaining flowering response in the 2nd IMN at three locations varying from 14°N to 49°N latitude.Contribution No 7516 from the Missouri Agricultural Experiment Station.     

A stability analysis of time to flowering as a screen for responsiveness to temperature and photoperiod in cowpea (Vigna unguiculata)

Summary Twenty-one genotypes of cowpea (Vigna unguiculata), comprising landraces and varieties, were grown in 22 photothermal environments in Nigeria and Niger, West Africa, and a stability analysis of days from sowing to flowering (f) was carried out. Cowpeas are rarely insensitive to photoperiod; they are typically quantitative shortday plants wherein f is delayed when photoperiod (P) is longer than the critical photoperiod (P _c ). Therefore, in order to quantify genotypic variation in temperature sensitivity, genotype f was regressed against the mean trial f in circumstances where P c (i.e. approximately 13 hd^-1) and mean temperature (T) was between 19° and 28° C. Correspondingly, in order to assess genotypic variation in photoperiod sensitivity, trials where T was near optimal (25°–28° C) but where P ranged from 10–14.5 hd^-1 were used. These stability analyses detected no significant differences (P>0.05) between genotypes 9n temperature sensitivity but revealed significant differences (P<0.001) in photoperiod sensitivity. Regression coefficients from the stability analysis were strongly correlated (r=0.94, 19df) with a photoperiod sensitivity constant, c, determined from a photothermal flowering model. A stability analysis of f from field trials can therefore identify and quantify genotypic variation in response to temperature and photoperiod in cowpea.Abbreviations f days from sowing to flowering - P mean photoperiod - P _c critical photoperiod - P _ce ceiling photoperiod - T mean temperature - T _b base temperature - T _o optimum temperature - SDP short-day plant     

Characterizations and molecular mapping of a novel dominant semi-dwarf gene Sdd(t) in rice (Oryza sativa)

By nitrogen ion implanting, we obtained a semi‐dwarf mutant from a japonica rice cultivar Y98148, designated as Y98149. The genetic analysis of Y98149 indicated that the semi‐dwarf phenotype was controlled by a single dominant gene, Sdd(t). We show that Y98149 reduced plant height mainly via inhibiting the first, second and third internode elongation. Based on this dwarfing pattern, the mutant could be grouped into dn‐type dwarf defined by Takeda [Gamma Field Symp. (1977) Vol. 16, PP. 1–18] . In addition, the Sdd(t) gene was sensitive to gibberellin (GA) based on the response to extraneous GA₃ and the quantitative determination of endogenous GA₁ and GA₄. To map the Sdd(t) gene, we tested molecular markers by bulk segregant analysis. The Sdd(t) gene was localized to a 6.4 cM‐interval on the short arm of chromosome 6, flanked by two sequence‐tagged site markers S9 and S13.     

Molecular mapping and identification of candidate gene conferring organophosphate-sensitive reaction in sorghum (Sorghum bicolor)

Some sorghum cultivars are sensitive to organophosphate insecticides, which cause red to purple injury spots and, in severe cases, leaf death. Sensitivity to organophosphates is conditioned by a single locus on chromosome 5. We constructed a high-density genetic map around the locus, termed osr, using DNA markers, and delimited osr to a 377-kb region on the short arm of chromosome 5. Sequence analysis of this region predicted 19 gene candidates. Four of the candidates are homologous to a disease resistance NBS-LRR gene. mRNA-Seq analysis of gene expression and SNPs from two resistant cultivars (‘JN43’ and ‘Greenleaf’) and one sensitive cultivar (‘Nakei MS3B’) suggest that one or more members of this NBS-LRR gene family are osr. Our results suggested that the recessive allele of osr results in sensitivity to OP insecticides.     

大鲵虹彩病毒-LY株主要衣壳蛋白基因克隆和分子特征研究

【目的】明确大鲵虹彩病毒-LY株主要衣壳蛋白（mcp）基因分子特征和我国不同CGSIV毒株mcp 基因变异及病毒的系统进化关系。【方法】克隆了CGSIV-LY株 mcp基因,并运用生物信息学软件对获得的基因信息进行了分析。【结果】CGSIV-LY 株mcp基因全长1392bp,可编码463个氨基酸。预测蛋白质分子量为50.03ku,理论等电点是5.75,为亲水性可溶蛋白。CGSIV-LY 株mcp不含有信号肽;没有跨膜区存在;抗原表位预测显示抗原性良好;结构预测显示,存在8个潜在的N-糖基化位点,存在17个潜在的O-糖基化位点和20个潜在的磷酸化位点。CGSIV-LY 株 mcp二级结构中无β-折叠,无规则卷曲占57.66%,延伸链占31.11%,α- 螺旋占11.23%,主要以延伸链和无规则卷曲为主。氨基酸序列包含3个结构域：氨基酸N末端,氨基酸C末端和capsid_NCLDV保守区结构域,并在氨基酸序列的第414~436区存在一个低复杂度域。氨基酸序列多重比对和基于mcp氨基酸序列构建的蛙病毒属成员系统进化树分析结果显示,包括CGSIV-LY 株在内的我国出现的不同CGSIV毒株之间mcp 基因差异很小,为平行进化关系,共同聚为蛙病毒属成员独立的一支。【结论】CGSIV-LY 株 mcp为可溶性亲水蛋白,具有良好的抗原性和较为丰富的潜在糖基化位点和磷酸化位点。其蛋白二级结构以延伸链和无规则卷曲为主。我国出现的不同CGSIV毒株mcp基因差异很小,应具有基本一致的分子结构和特征。     

Development and validation of a robust KASP marker for zt2 locus in faba bean (Vicia faba)

Faba bean has the potential to become a key food and feed protein crop in many areas of the world. The presence of tannins in its seed coat has limited the deployment of this crop as feed and food. The expression of either of the two recessive genes, zt1 and zt2, causes a great reduction of tannins from the seed coat and results in a white flower phenotype. Molecular markers linked to these loci are fundamental tools for speeding up the breeding of low-tannin varieties. The main aim of this study was to develop and validate a robust molecular marker linked to the zt2 locus. We used 176 recombinant inbred lines of the Disco/2 × ILB 938/2 cross at F₆ and genotyped those using 257 SNP (single nucleotide polymorphism) markers. An SNP marker associated with zt2 locus was found on faba bean chromosome 3 and was used to develop a high-throughput low-cost KASP (kompetitive allele-specific PCR) marker. The KASP marker can successfully discriminate low-tannin faba beans carrying zt2 from those carrying zt1 and wild-type alleles.     

Converting restriction fragment length polymorphism to single‐strand conformation polymorphism markers and its application in the fine mapping of a trichome gene in cotton

A well‐characterized and systematically organized collection of genetic markers is crucial in the study of any crop species. It is the basis of map‐based gene cloning and crop improvements through marker‐assisted selections. Single‐strand conformation polymorphism (SSCP) has been a robust way of discovering new polymorphisms in marker development without the requirement of sequencing. Here, we report the first approach of applying SSCP marker discovery methods in the genetic map construction and gene mapping of cotton species. A total of 80 restriction fragment length polymorphism (RFLP) markers were selected from a region on published cotton genetic maps around the T1 gene related to cotton trichome. Among the 80 RFLPs, 28 showed polymorphisms through SSCP, showing a polymorphic rate of approximately 35%, which is much higher than that of simple sequence repeat (SSR) markers in the same region (7.8%). By integrating these newly generated SSCP markers, a detailed genetic map was reconstructed around this region using an F₂ population derived from a cross between Gossypium arboreum and G. herboceum. The reconstructed region comprises 22 SSCP markers, eight SSR markers and the T1 gene, spanning 21.6 cM. The marker order of the new map agrees well with published reference RFLP maps. The above results suggest that SSCP method can be applied very efficiently and reliably to the marker development of cotton genomes. It will prove to be even more valuable and robust after the public release of cotton whole‐genome sequences.     

High-resolution mapping revealed a 1.3-Mbp genomic inversion in Ssi1, a dominant semidwarf gene in rice (Oryza sativa)

Dwarf or semidwarf characters are an important trait for crop breeding as they provide lodging resistance. The rice mutant line DMF-1 has a dm-type semidwarf phenotype and high-lodging resistance controlled by the dominant gene, Short second internode 1 ( Ssi1 ). To elucidate the mechanism of reducing culm length in DMF-1, we sought to identify the Ssi1 gene by positional cloning using the chromosome segment substitution line as a crossing parent. As a result of high-resolution mapping, we found a 1.3-Mbp genomic inversion and a newly arranged gene in the Ssi1 locus. In this study, we report the high-resolution mapping and physical mapping of Ssi1 . We also discuss the possible function of a novel rearranged Ssi1 gene for the dominant dm-type semidwarf phenotype.     

Development of a SCAR marker linked with a MYMV resistance gene in mungbean (Vigna radiata L. Wilczek)

Yellow mosaic disease (YMD) caused by mungbean yellow mosaic virus (MYMV) is the most important disease of mungbean, causing great yield loss. The present investigation was carried out to study the inheritance and identify molecular markers linked with MYMV resistance gene by using F₁, F₂ and 167 F_2 : 8 recombinant inbred lines (RILs) developed from the cross ‘TM‐99‐37’ (resistant) × Mulmarada (susceptible). The F₁ was susceptible, F₂ segregated in 3S:1R phenotypic ratio and RILs segregated in 1S:1R ratio in the field screening indicating that the MYMV resistance gene is governed by a single recessive gene. Of the 140 RAPD primers, 45 primers showing polymorphism in parents were screened using bulked segregant analysis. Three primers amplified specific polymorphic fragments viz. OPB‐07_600, OPC‐06₁₇₅₀ and OPB‐12₈₂₀. The marker OPB‐07₆₀₀ was more closely linked (6.8 cM) with a MYMV resistance gene as compared to OPC‐06₁₇₅₀ (22.8 cM) and OPB‐12₈₂₀ (25.2 cM). The resistance‐specific fragment OPB‐07₆₀₀ was cloned, sequenced and converted into a sequence‐characterized amplified region (SCAR) marker and validated in twenty genotypes with different genetic backgrounds.     

水稻圆粒基因RS的鉴定和定位

阐明水稻籽粒大小相关基因的遗传和分子机制对水稻产量形成具有重要意义。利用甲基磺酸乙酯(ethyl methanesulfonate, EMS)诱变粳稻品种宁粳3号筛选获得圆粒突变体round seed (rs)。遗传分析表明,突变体rs圆粒表型由单隐性核基因控制。颖壳扫描电镜观察发现,rs籽粒变圆主要是细胞数目改变导致的。在突变体rs中,细胞周期相关基因的表达较野生型显著升高。将RS定位在第3染色体短臂标记RM3413与N3-5之间,物理距离约589 kb。RS突变影响BR信号途径,改变了粒型相关基因的表达。本研究有助于阐明水稻籽粒发育的分子机制。     

水稻类病斑早衰突变体lmps1的表型鉴定与基因定位

经甲基磺酸乙酯(EMS)诱变优良籼型水稻恢复系缙恢10号,获得一个稳定遗传的水稻类病斑早衰突变体lmps1(lesion mimic and premature senescence 1)。该突变体苗期表型正常,分蘖早期出现褐色类病斑,且斑点数目随植株生长而增多,孕穗期叶片开始萎黄衰老。与野生型相比,突变体lmps1的每穗总粒数下降8%(P0.05),株高、穗长、有效穗数、每穗实粒数、结实率以及千粒重分别下降14.3%、24.3%、27.2%、50%、45.7%与14.5%,差异均达极显著水平(P0.01)。遮光处理表明,突变体lmps1的类病斑性状受光照诱导。孕穗期叶片光合色素含量下降且光合效率降低, H2O2含量增加,抗氧化酶SOD和CAT的活性显著降低。透射电镜观察结果显示,突变体lmps1叶肉细胞中叶绿体数目减少,叶绿体的类囊体片层结构损伤降解。qRT-PCR结果显示,突变体lmps1中防卫反应相关基因除POX22.3表达量降低外,POC1、PAL、PBZ1、PR1、NPR1、PR5表达量均极显著高于野生型。遗传分析表明突变体lmps1的类病斑早衰性状受1对隐性核基因控制,利用西农1A与突变体lmps1杂交所得F2群体中的突变株,将目标基因定位于第7染色体长臂端粒附近约167.3 kb的物理区段内。     

Identification and mapping of a novel Turnip mosaic virus resistance gene TuRBCS01 in Chinese cabbage (Brassica rapa L.)

We aimed to identify Turnip mosaic virus (TuMV) resistance genes in Chinese cabbage by analysing the TuMV resistance of 43 P₁ (resistant), 88 P₂ (susceptible), 26 F₁, 104 B₁ (F₁ × P₁), 108 B₂ (F₁ × P₂) and 509 F₂ individuals. All parents and progeny populations were mechanically inoculated with TuMV‐C4. Both F₁ and B₁ populations showed TuMV resistance. Resistant: susceptible ratios in the B₂ and F₂ populations were 1 : 1 and 3 : 1, respectively. TuMV resistance in P₁ was controlled by a dominant gene, TuRBCS01. Bulked segregation analysis was performed to identify simple sequence repeat or insertion or deletion markers linked to TuRBCS01. Data from 108 B₂ individuals with resistant or susceptible phenotypes were analysed using mapmake r/exp 3.0. Polymorphic marker sequences were blast searched on http://brassicadb.org/brad/ . TuRBCS01 was found to be linked to eight markers: SAAS_mDN192117a_159 (3.3 cM), SAAS_mDN192117b_196 (4.0 cM), SAAS_mDN192403_148 (13.0 cM), SAAS_mGT084561_233 (6.8 cM), BrID10723 (3.3 cM), mBr4041 (3.3 cM), SAAS_mBr4055_194 (2.6 cM) and mBr4068 (4.0 cM). Further, TuRBCS01 was mapped to a 1.98‐Mb region on chromosome A04 between markers BrID10723 and SAAS_mBr4055_194.     

Identification and inheritance of a new gene for powdery mildew resistance in mungbean (Vigna radiata L. Wilczek)

Powdery mildew (PM) is one of the important foliar diseases of mungbean. Resistance sources have been identified in India and the inheritance studies showed that complete resistance (RO) was controlled by two dominant genes, Pm1 , Pm2 . The breakdown of complete resistance (RO) into moderate resistance (R2) by race-2 (Akola) has been reported. It is assumed that the change in resistance reaction is due to a mutation in the pathogen. The present investigation was carried out with a view to screen germplasm, cultivars and mutants for identification of complete resistance (RO) sources against race-2 and to study their inheritance. 'Mulmarada', a local mungbean cultivar from Maharashtra state of India was identified as a complete resistance (RO) source for race-2. The inheritance of Mulmarada's resistance (RO) was studied. The F₁ and the segregation in F₂ and F₃ showed that the complete resistance (RO) in 'Mulmarada' is controlled by a single dominant gene, which is different from the earlier identified Pm1 and Pm2 resistance genes. Mulmarada's resistance gene is designated as Pm3 for PM resistance.     

Chromosome location and microsatellite markers linked to a powdery mildew resistance gene in wheat line 'Lankao 90(6)'

Wheat lines known as 'Lankao 90(6)', derived from the cross 'Mzalenod Beer' (hexaploid triticale)/'Baofeng 7228'//'90 Xuanxi', carry a recessive powdery mildew resistance gene temporarily named PmLK906 . Gene PmLK906 appears to be different from known wheat powdery mildew resistance genes. PmLK906 was tagged using microsatellite markers in a segregating population derived from the cross 'Chinese Spring'/'Lankao 90(6)21-12'. The dominant microsatellite marker Xgwm265-2AL was linked in repulsion with PmLK906 at a genetic distance of 3.72 cM, whereas the co-dominant Xgdm93-2AL was linked to PmLK906 at a genetic distance of 6.15 cM. Both markers were placed on chromosome arm 2AL using 'Chinese Spring' nulli-tetrasomic lines. The recessive PmLK906 has a different specificity to the dominant resistance alleles located at the Pm4 locus and appeared to be located to a locus different from Pm4 .     

Inheritance and molecular mapping of restorer‐of‐fertility (Rf) gene in A2 hybrid system in pigeonpea (Cajanus cajan)

Inheritance of fertility restorer gene in pigeonpea was studied using F₂ and BC₁F₁ populations derived from cross AL103A × IC245273. It was found to be controlled by single dominant gene. Out of 228 SSR primer pairs, 33 primer pairs showed parental polymorphism, while four primers were found polymorphic in bulk segregant analysis (BSA). These four primers viz., CcM 1615, CcM 0710, CcM 0765 and CcM 1522 were used for genotyping of F₂ population and were found to be placed at 3.1, 5.1, 28.1 and 45.8 cM, respectively. Two of them, CcM 1615 and CcM 0710, evinced clear and unambiguous bands for fertility restoration in F₂ population. The Rf gene was mapped on linkage group 6 between the SSR markers CcM 1615 and CcM 0710 with the distances of 3.1 and 5.1 cM, respectively. The accuracy of the CcM 1615 was validated in 18 restorers and six maintainer lines. The marker CcM 1615 amplified in majority of male restorer lines with a selection accuracy of 91.66%.