Structural homology between semidwarfism-related proteins and glutelin seed protein in rice (Oryza sativa L.)

Summary Two semidwarfism-related proteins, SRP-1 and SRP-2, were detected as major spots in a long-culm rice cultivar, Norin 29 and its semidwarf near-isogenic line, SC-TN1, respectively, by two-dimensional gel electrophoresis (2D-PAGE). The testcross showed that SRP-1 and SRP-2 are controlled by codominant alleles, Srp-1 and Srp-2, respectively, at a single locus Srp. This locus was considered to be closely linked with the semidwarfing gene locus sd-1. SRP-1 and SRP-2 were separated by 2D-PAGE, electroblotted onto a polyvinylidene difluoride membrane, and sequenced by a gas-phase protein sequencer. The N-terminal amino acid sequences, however, could not be determined due to the blockage of the N-terminals of these proteins. After removal of the N-terminal residue with pyroglutamyl peptidase given to the membrane, the amino acid sequence in the N-terminal region was determined. The N-terminal and internal amino acid sequences of SRP-1 and SRP-2 were highly homologous with those of the glutelin -subunits of seed endosperm storage protein, which were deduced by the cDNA sequences. In the seed endosperms of Norin 29 and SC-TN1, a total of eight glutelin -subunits was identified by 2D-PAGE. The amino acid sequences in the N-terminal and internal regions of these proteins were determined. This experiment confirmed that SRP-1 and SRP-2 are almost identical in structure with the glutelin _5a- and _5b-subunits, respectively, which were identified in several organs such as endosperms, embryos, and leaves, unlike the other glutelin -subunits.     

水稻半矮生基因sd—1的遗传性状表现：Ⅲ.半矮生与穗粒数的结合

半矮生基因ｓｄ－１有抗倒伏和改善株型的效果,广泛存在于世界各地的水稻丰产品种中,最近发现该基因具有减少穗长和千粒重的副作用。为澄清此副作用,能否通过遗传背景的改良得以克服,进而培育成粳稻型的半矮生大穗品咱,本研究用高秆品种农林２９号及其半矮生纯合系ＳＣ－ＴＮ１和大穗品种Ａｋｅｎｏｈｏｓｈｉ的杂种进行了分析。用Ｆ４代系统的实验结果表明,半矮生系统的穗长较高秆系统的为小。但是,由于半矮生系统的枝梗数。     

水稻半矮生基因sd－1的遗传性状表现──Ⅳ．半矮生性与大粒性的结合

为克服水稻半矮生基因ｓｄ－１减小粒重的副作用,培育了半矮生粳稻型大粒品种。本研究用具有大粒基因ｌｋ－ｆ的高秆品种房吉和具有半矮生基因ｓｄ－１系统ＳＣ－ＴＮ１的杂种进行了鉴定分析。结果表明,选育的半矮生系统的千位重均较ＳＣ－ＴＮ１有所提高,并出现了千粒重３０克以上的系统。亲子代的相关分析表明,粒长间有高度的正相关。充分说明,ｓｄ－１的半矮生性和大粒性的结合是可能的。因此指出,通过选择适当的大粒种质资源与ｓｄ－１基因组合,使半矮生性的抗倒伏和大粒的丰产性一体化,可以培育成丰产性更高的粳稻品种。     

Molecular mapping of two semidwarf genes in an indica rice variety Aitaiyin3 (Oryza sativa L.)

Genetic analysis established that Aitaiyin3, a dwarf rice variety derived from a semidwarf cultivar Taiyin1, carries two recessive semidwarf genes. By using simple sequence repeat (SSR) markers, we mapped the two semidwarf genes, sd-1 and sd-t2 on chromosomes 1 and 4, respectively. Sd-t2 was thus named because the semidrawf gene sd-t has already been identified from Aitaiyin 2 whose origin could be traced back to Taiyin1. The result of the molecular mapping of sd-1 gene revealed it is linked to four SSR markers found on chromosome 1. These markers are: RM297, RM302, RM212, and OSR3 spaced at 4.7 cM, 0 cM, 0.8cM and 0 cM, respectively. Sd-t2 was found to be located on chromosome 4 using five SSR markers: two markers, SSR332 and RM1305 located proximal to sd-t2 are spaced 11.6 cM, 3.8 cM, respectively, while the three distally located primers, RM5633, RM307, and RM401 are separated by distances of 0.4 cM, 0.0 cM, and 0.4 cM, respectively. __________ Translated from Acta Genetica Sinica, 2005, 32 (2) [译自: 遗传学报, 2005,32(2)]     

高秆突变体Mh—1的株高遗传研究

Ｍｈ－１是从矮秆品种桂朝２号辐射诱变后代中产生的高秆突变体。用Ｍｈ－１与ｓｄ－１矮秆、非ｓｄ－１矮秆和普通高秆材料杂交,通过对Ｆ１、Ｆ２、Ｆ３等世代以及测交后代的株高进行遗传分析,结果表明,Ｍｈ－１的高秆特性是由１对隐性抑制基因控制的,该抑制基因能调节ｓｄ－１基因的表达,而对由非ｓｄ－１基因控制的矮秆没有抑制作用,这一隐性抑制基因暂时被定名为ｉ－ｓｄ－１（ｔ）。还讨论了该基因的遗传学意义和可能的育     

Molecular mapping of two semidwarf genes in an indica rice variety Aitaiyin3 (Oryza sativa L.)

Genetic analysis established that Aitaiyin3,a dwarf rice variety derived from a semidwarf cultivar Taiyin1,carries two recessive semidwarf genes.By using simple sequence repeat(SSR)markers,we mapped the two semidwarf genes,sd-1 and sd-t2 on chromosomes 1 and 4,respectively.Sd-t2 was thus named because the semidrawf gene sd-t has already been identified from Aitaiyin 2 whose origin could be traced back to Taivin1.The result of the molecular mappingof sd-1 gene revealed it is linked to four SSR markers found on chromosome 1.These markers are:RM297,RM302,RM212,and OSR3 spaced at 4.7 cM,0 cM,0.8cM and 0 cM,respectively.Sd-t2 was found to be located on chromosome 4 using five SSR markers:two markers,SSR332 and RM1305 located proximal to sd-t2 are spaced 11.6 cM,3.8 cM,respectively,while the three distally located primers,RM5633,RM307,and RM401 are separated by distances of 0.4 cM,0.0 cM,and 0.4 cM,respectively.     

Identification of pistil-specific proteins associated with three self-incompatibility alleles in Solanum chacoense

Summary Pistil proteins associated with three different S-alleles of the self-incompatibility locus (S locus) in Solanum chacoense have been identified which cosegregated with their respective S alleles in a series of genetic crosses involving six S. chacoense plants, their F₁ progeny, and backcrosses. The molecular weights of these three S-allele-associated proteins, designated S₁ S₂, and S₃, were 29 kDa, 30 kDa, and 31 kDa, respectively. They were all basic proteins with a similar pI of approximately 8.6. They have been found only in the stigma and style of the pistil where their maximum synthesis was reached at one day before anthesis. Their rate of synthesis in both self- and cross-pollinated pistils was the same as that in the unpollinated pistil until 2 days after pollination.On sabbatical leave from Laboratoire de Genetique et Physiologie du Developpement des Plantes, C.N.R.S., F-91190 Gifsur-Yvette, France     

GA-20 oxidase as a candidate for the semidwarf gene sdw1/denso in barley

The barley sdw1/denso gene not only controls plant height but also yield and quality. The sdw1/denso gene was mapped to the long arm of chromosome 3H. Comparative genomic analysis revealed that the sdw1/denso gene was located in the syntenic region of the rice semidwarf gene sd1 on chromosome 1. The sd1 gene encodes a gibberellic acid (GA)-20 oxidase enzyme. The gene ortholog of rice sd1 was isolated from barley using polymerase chain reaction. The barley and rice genes showed a similar gene structure consisting of three exons and two introns. Both genes share 88.3% genomic sequence similarity and 89% amino acid sequence identity. A single nucleotide polymorphism was identified in intron 2 between barley varieties Baudin and AC Metcalfe with Baudin known to contain the denso semidwarf gene. The single nucleotide polymorphism (SNP) marker was mapped to chromosome 3H in a doubled haploid population of Baudin × AC Metcalfe with 178 DH lines. Quantitative trait locus analysis revealed that plant height cosegregated with the SNP. The sdw1/denso gene in barley is the most likely ortholog of the sd1 in rice. The result will facilitate understanding of the molecular mechanism controlling semidwarf phenotype and provide a diagnostic marker for selection of semidwarf gene in barley. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Sequence variability and gene structure at the self-incompatibility locus of Solanum tuberosum

Summary Allelic complexity is a key feature of self-incompatibility (S) loci in gametophytic plants. We describe in this report the allelic diversity and gene structure of the S locus in Solanum tuberosum revealed by the isolation and characterization of genomic and cDNA clones encoding S-associated major pistil proteins from three alleles (S ₁, S _r1, S ₂). Genomic clones encoding the S₁ and S₂ proteins provide evidence for a simple gene structure: Two exons are separated by a small intron of 113 (S ₁) and 117 by (S ₂). Protein sequences deduced from cDNA clones encoding S₁ and S_r1 proteins show 95% homology. 15 of the 25 residues that differ between these S ₁and S _r1alleles are clustered in a short hypervariable protein segment (amino acid positions 44–68), which corresponds in the genomic clones to DNA sequences flanking the single intron. In contrast, these alleles are only 66% homologous to the S ₂allele, with the residues that differ between the alleles being scattered throughout the sequence. DNA crosshybridization experiments identify a minimum of three classes of potato S alleles: one class contains the alleles S ₁, S _r1and S ₃, the second class S ₂and an allele of the cultivar Roxy, and the third class contains at present only S ₄. It is proposed that these classes reflect the origin of the S alleles from a few ancestral S sequence types.     

Variation and classification of B low-molecular-weight glutenin subunit alleles in durum wheat

 The B low-molecular-weight (LMW) glutenin subunit composition of a collection of 88 durum wheat cultivars was analyzed. Extensive variation has been found and 18 different patterns were detected. Each cultivar exhibited 4–8 subunits, and altogether 20 subunits of different mobility were identified. The genetic control of all these subunits was determined through the analysis of nine F₂ populations and one backcross. Five subunits were controlled at the Glu-A3 locus, 14 at Glu-B3 and 1 at Glu-B2. At the Glu-A3 locus each cultivar possessed from zero to three bands and eight alleles were identified. At the Glu-B3 locus each cultivar showed four or five bands and nine alleles were detected. Only one band was encoded by the Glu-B2 locus. A nomenclature for these alleles is proposed and the relationship between them and the commonly used LMW-model nomenclature is discussed. Received: 10 February 1997 / Accepted: 25 April 1997     

RFLP mapping of the genes controlling hybrid breakdown in rice (Oryza sativa L.)

 Complementary recessive genes hwd1 and hwd2 controlling hybrid breakdown (weakness of F₂ and later generations) were mapped in rice using RFLP markers. These genes produce a plant that is shorter and has fewer tillers than normal plants when the two loci have only one or no dominant allele at both loci. A cultivar with two dominant alleles at the hwd1 locus and a cultivar with two dominant alleles at the hwd2 locus were crossed with a double recessive tester line. Linkage analysis was carried out for each gene independently in two F₂ populations derived from these crosses. hwd1 was mapped on the distal region of rice genetic linkage map for chromosome 10, flanked by RFLP markers C701 and R2309 at a distance of 0.9 centiMorgans (cM) and 0.6 cM, respectively. hwd2 was mapped in the central region of rice genetic linkage map for chromosome 7, tightly linked with 4 RFLP markers without detectable recombination. The usefulness of RFLP mapping and map information for the genes controlling reproductive barriers are discussed in the context of breeding using diverse rice germplasm, especially gene introduction by marker-aided selection.     

Quantitative real-time PCR to determine allele number for the astringency locus by analysis of a linked marker in Diospyros kaki Thunb

Persimmon (Diospyros kaki Thunb.) is a polyploidy fruit tree species of economic importance to East Asia. Natural astringency loss is an important trait in persimmon breeding programs. Quantitative real-time PCR was used to determine the number of AST/ast alleles for fruit astringency in persimmon (D. kaki Thunb.). To this end, the cultivar Jiro was transformed with one or two copies of a gene encoding NADP-dependent sorbitol-6-phosphate dehydrogenase (S6PDH), which was used as a standard for measuring the allele number of a sequenced marker tightly linked to the recessive ast locus for nonastringency. Primers for markers linked to the AST or ast allele were then used to measure the AST to ast ratio directly in the progeny of a full-sib cross. From determination of the AST to ast ratio and the results of the S6PDH copy number, the number of AST and ast alleles at the AST/ast locus was estimated. This research supported the hypothesis that D. kaki is a hexaploid with six AST and/or ast alleles. In addition to the determination of the allelic status of the AST locus, the application of real-time PCR for confirmation of the ploidy level and allelic composition of target genes in autopolyploids or allopolyploids was demonstrated.     

Leaf rust resistance gene Lr1, isolated from bread wheat (Triticum aestivum L.) is a member of the large psr567 gene family

In hexaploid wheat, leaf rust resistance gene Lr1 is located at the distal end of the long arm of chromosome 5D. To clone this gene, an F₁-derived doubled haploid population and a recombinant inbred line population from a cross between the susceptible cultivar AC Karma and the resistant line 87E03-S2B1 were phenotyped for resistance to Puccinia triticina race 1-1 BBB that carries the avirulence gene Avr1. A high-resolution genetic map of the Lr1 locus was constructed using microsatellite, resistance gene analog (RGA), BAC end (BE), and low pass (LP) markers. A physical map of the locus was constructed by screening a hexaploid wheat BAC library from cultivar Glenlea that is known to have Lr1. The locus comprised three RGAs from a gene family related to RFLP marker Xpsr567. Markers specific to each paralog were developed. Lr1 segregated with RGA567-5 while recombinants were observed for the other two RGAs. Transformation of the susceptible cultivar Fielder with RGA567-5 demonstrated that it corresponds to the Lr1 resistance gene. In addition, the candidate gene was also confirmed by virus-induced gene silencing. Twenty T ₁ lines from resistant transgenic line T ₀-938 segregated for resistance, partial resistance and susceptibility to Avr1 corresponding to a 1:2:1 ratio for a single hemizygous insertion. Transgene presence and expression correlated with the phenotype. The resistance phenotype expressed by Lr1 seemed therefore to be dependant on the zygosity status. T ₃-938 sister lines with and without the transgene were further tested with 16 virulent and avirulent rust isolates. Rust reactions were all as expected for Lr1 thereby providing additional evidence toward the Lr1 identity of RGA567-5. Sequence analysis of Lr1 indicated that it is not related to the previously isolated Lr10 and Lr21 genes and unlike these genes, it is part of a large gene family. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. The Canadian Crown's right to retain a non-exclusive, royalty-free licence in and to any copyright is acknowledged.     

Esterase-29 (ES-29): Biochemical characterization and control by two independent gene loci of a testosterone-dependent mouse serum esterase

Biochemistry and genetics of a testosterone-dependent murine serum esterase designated esterase-29 (ES-29) are described. The enzyme was identified after disc electrophoresis and subsequent staining for esterase using -naphthyl acetate as the substrate. It was inhibited by bis-p-nitrophenyl phosphate and was resistant top-chlorophenylsulphonate and hence was classified as carboxylesterase EC 3.1.1.1. The molecular mass was estimated to be about 130 kDa. It was shown that ES-29 is under the control of two independent genes. The first, termed Es-29, is suggested to be a structural locus, linked to the cluster-2 esterase loci on chromosome 8. Three alleles atEs-29, Es-29 ^a, Es-29^b, andEs-29 ^care distinguished, which determine absence (SEG/1), strong activity (BALB/cJ), and low activity (MOLH/Fre), respectively. The second locus, termedMse-1 (serum esterase modifying factor), was found to be closely linked toPre-2 on chromosome 12 and is suggested to be a modifying or regulatory gene. Two alleles were distinguished,Mse-1 ^a(BALB/cJ) andMse-1 ^m(MOL3/JA, CasBgr), which determine whether ES-29 appears as a single band or a double band, respectively.Mse-1 ^mis dominant toMse-1 ^a.This work was supported by the Deutsche Forschungsgemeinschaft. This is communication No. 70 of a research program devoted to the cellular distribution, genetics, and regulation of nonspecific esterases.     

Genes for dwarfing and photoperiod flowering response inPharbitis nil choisy

Dwarfing and sensitivity to the duration of a single inductive dark period for flowering ofPharbitis nil in F₂ progeny of a cross between the tall strain Tendan, and the dwarf, Kidachi appear to be controlled by the alleles at two independent loci. Progeny of a similar cross between the tall strain Violet and the dwarf Kidachi at F₂ and F₃ also showed single locus segregation for tall: dwarf plants. In this cross, differences in photoperiodic response could be identified in F₃ families but they were not simply inherited. There was some evidence of difficulties with classification of the F₂ plants, but also, the flowering of the F₁ between the two less sensitive strains Tendan and Violet indicated complex inheritance of their photoperiodic response. Complementary dominant alleles at three independent loci may be necessary for flowering in even shorter dark periods with the sensitive strain Kidachi. The dwarf strain Kidachi has a reduced gibberellin (GA) content (Barendse and Lang 1972), it flowers in a short dark period without terminal flowering, and it responds positively to GA application both for flowering and growth. However, since control of dwarfing and photoperiodic sensitivity can be separated genetically, there is no strick link between the gibberellin responsiveness of Kidachi for its growth and flowering. Despite the complexity of flowering genetics in Violet×Kidachi, a short-dark-period-sensitive, terminal flowering and tall F₇ line was obtained in a pedigree previously held heterozygous for the dwarf: tall character but not selected for flowering time. Thus, flowering in a short dark period can also be obtained in the presence of the non-dwarfing allele from strain Violet, again demonstrating genetic independence.     

Genetic mapping and protein product diversity of the self-incompatibility locus in wild tomato (Lycopersicon peruvianum)

Phenotypic diversity of self-incompatibility (S) alleles within nine natural populations ofLycopersicon peruvianum was investigated. Only 7 incompatible responses were observed of a total of 276 unique combinations tested, on the basis of controlled pollinations, indicating the large number of alleles that exist within these populations. Molecular weight polymorphism for specific major stylar proteins observed on SDS-PAGE was also evident in two of the populations examined. Five proteins were shown to map to theS locus and to be associated with differentS alleles through controlled pollinations and segregation of the proteins. Two of theseS related proteins had been described previously in terms of spatial and temporal expression consistent with their involvement in self-incompatibility (Mauet al., Planta 169, 184–191, 1986). A mapping population derived from a fully compatible cross was used to establish linkage of theS locus to two DNA markers,CD15 andTG184, that lie on chromosome 1. The order of the markers and estimates of map distances are given.     

Mapping of the QTL (quantitative trait locus) conferring partial resistance to leaf blast in rice cultivar Chubu 32

The rice cultivar Chubu 32 possesses a high level of partial resistance to leaf blast. The number and chromosomal location of genes conferring this resistance were detected by restriction fragment length polymorphism (RFLP) linkage mapping and quantitative trait locus (QTL) analysis. For the mapping, 149 F₃ lines derived from the cross between rice cultivar Norin 29, with a low level of partial resistance, and Chubu 32 were used, and their partial resistance to leaf blast was assessed in upland nurseries. A linkage map covering six chromosomes and consisting of 36 RFLP markers was constructed. In the map, only one significant QTL (LOD>2.0) for partial resistance was detected on chromosome 11. This QTL explained 45.6% of the phenotypic variation. The segregation ratio of the F3 lines was 3:1 for partial resistance to susceptibility. These results suggest that the partial resistance in Chubu 32 is controlled by a major gene. Received: 15 March 2001 / Accepted: 13 August 2001     

Differential regulation of waxy gene expression in rice endosperm

Summary In order to examine the effects of different alleles on the gene expression at the waxy locus, the Wx gene product which controls the synthesis of amylose was isolated from endosperm starch of rice plants and analysed by electrophoretic techniques. The major protein bound to starch granules was absent in most of waxy strains and increased with the number of Wx alleles in triploid endosperms, suggesting that the major protein is the Wx gene product. In addition to wx alleles which result in the absence or drastic reduction of the Wx gene product and amylose, differentiation of Wx alleles seemed to have occurred among nonwaxy rice strains. At least two Wx alleles with different efficiencies in the production of the major protein as well as amylose were detected. These alleles are discussed in relation to regulation of the gene expression.     

Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice

Genetic polymorphisms of ten microsatellite DNA loci were examined among 238 accessions of landraces and cultivars that represent a significant portion of the distribution range for both indica and japonica groups of cultivated rice. In all, 93 alleles were identified with these ten markers. The number of alleles varied from a low of 3 or 4 at each of four loci, to an intermediate value of 9–14 at five loci, and to an extra-ordinarily high 25 at one locus. The numbers of alleles per locus are much larger than those detected using other types of markers. The number of alleles detected at a locus is significantly correlated with the number of simple sequence repeats in the targeted microsatellite DNA. Indica rice has about 14% more alleles than japonica rice, and such allele number differences are more pronounced in landraces than in cultivars. The indica-japonica differentiation component accounted for about 10% of the diversity in the total sample, and twice as much differentiation was detected in cultivars as in landraces. About two-thirds as many alleles were observed in cultivars as in landraces; another two-thirds of the alleles in the cultivar group were found in modern elite cultivars or parents of hybrid rice. The majority of the simple sequence repeat (SSR) alleles that were present in high or intermediate frequencies in landraces ultimately survived into modern elite cultivars and hybrids. The greater resolving power and the efficient production of massive amounts of SSR data may be particularly useful for germplasm assessment and evolutionary studies of crop plants.     

The semidwarf gene,sd-1, of rice (Oryza sativa L.). I. Linkage with the esterase locus,Estl-2

The linkage relationship between the semidwarf gene (sd-1) and the isozyme locus EstI-2 was elucidated using segregating populations derived from crosses between several semidwarf testers and tall rice varieties. Bimodal distributions for culm length were observed in F₂ populations of three cross combinations, including Shiokari/Shiokari (sd-1), Taichung 65 (A,Pn,Pau)/Taichung 65 (sd-1), and Milyang 23/Kasalath. Taking the valley of the distribution curves as the dividing point, two height classes were apparent with a segregation ratio of 3 tall1 short, demonstrating this character to be under the control of a single recessive gene. An inheritance study of esterase isozymes, based on isoelectric focusing (IEF), showed that the EstI-2 locus had two active allozymes of monomeric structure and one null form, which were designated a, b, and n, respectively (Eun et al. 1990). Semidwarf testers such as Shiokari (sd-1), Taichung 65 (sd-1) and Milyang 23 have an active allozyme designated as EstI-2^aa, while the tall parents, Shiokari and Taichung 65 (A,Pn,Pau), have the active allozyme, EstI-2^bb, and Kasalath has a null form of the allozyme, EstI-2ⁿⁿ. By dividing F₂ populations based on EstI-2 allozyme patterns, culmlength distributions exhibited trimodal curves. Most of the short plants had the homozygous EstI-2^aa pattern of the short parents, most of the tall plants had the homozygous pattern, EstI-2^bb or EstI-2ⁿⁿ, and most of the intermediate plants had the heterozygous EstI-2^ab or EstI-2^an banding pattern. Einkage analysis indicated that sd-1 and EstI-2 were tightly linked. These findings were also confirmed by segregation analyses in F₃ progenies. No recombinants among 171 F₃ families from the Shiokari/Shiokari (sd-1) combination, five recombinants among 267 F₃ families from Taichung 65 (A,Pn,Pau)/Taichung 65(sd-1), and only two recombinants out of 237 F₃ families from Milyang 23/Kasalath, were found. The recombination values were 0, 1.87 and 0.8%, respectively.