Inheritance of seed coat color genes in <Emphasis Type="Italic">Brassica napus</Emphasis> (L.) and tagging the genes using SRAP,SCAR and SNP molecular markers

Seed coat color inheritance in Brassica napus was studied in F₁, F₂, F₃ and backcross progenies from crosses of five black seeded varieties/lines to three pure breeding yellow seeded lines. Maternal inheritance was observed for seed coat color in B. napus, but a pollen effect was also found when yellow seeded lines were used as the female parent. Seed coat color segregated from black to dark brown, light brown, dark yellow, light yellow, and yellow. Seed coat color was found to be controlled by three genes, the first two genes were responsible for black/brown seed coat color and the third gene was responsible for dark/light yellow seed coat color in B. napus. All three seed coat color alleles were dominant over yellow color alleles at all three loci. Sequence related amplified polymorphism (SRAP) was used for the development of molecular markers co-segregating with the seed coat color genes. A SRAP marker (SA12BG18388) tightly linked to one of the black/brown seed coat color genes was identified in the F₂ and backcross populations. This marker was found to be anchored on linkage group A9/N9 of the A-genome of B. napus. This SRAP marker was converted into sequence-characterized amplification region (SCAR) markers using chromosome-walking technology. A second SRAP marker (SA7BG29245), very close to another black/brown seed coat color gene, was identified from a high density genetic map developed in our laboratory using primer walking from an anchoring marker. The marker was located on linkage group C3/N13 of the C-genome of B. napus. This marker also co-segregated with the black/brown seed coat color gene in B. rapa. Based on the sequence information of the flanking sequences, 24 single nucleotide polymorphisms (SNPs) were identified between the yellow seeded and black/brown seeded lines. SNP detection and genotyping clearly differentiated the black/brown seeded plants from dark/light/yellow-seeded plants and also differentiated between homozygous (Y2Y2) and heterozygous (Y2y2) black/brown seeded plants. A total of 768 SRAP primer pair combinations were screened in dark/light yellow seed coat color plants and a close marker (DC1GA27197) linked to the dark/light yellow seed coat color gene was developed. These three markers linked to the three different yellow seed coat color genes in B. napus can be used to screen for yellow seeded lines in canola/rapeseed breeding programs.     

Pigmentation in Black-boned sheep (Ovis aries): association with polymorphism of the MC1R gene

Variations in vertebrate skin and hair color are due to varied amounts of eumelanin (brown/black) and phaeomelanin (red/yellow) produced by the melanocytes. The melanocortin 1 receptor (MC1R) is a regulator of eumelanin and phaeomelanin production in the melanocytes, and MC1R mutations causing coat color changes are known in many vertebrates. We have sequenced the entire coding region of the MC1R gene in Black-boned, Nanping indigenous and Romney Marsh sheep populations and found two silent mutation sites of A12G and G144C, respectively. PCR-RFLP of G144C showed that frequency of allele G in Black-boned, Nanping indigenous and Romney Marsh sheep was 0.818, 0.894 and 0, respectively. Sheep with GG genotype had significantly higher (P < 0.05) tyrosinase activity than sheep with CC genotype in the all investigated samples. Moreover, there was significant effect of MC1R genotype on coat color, suggesting that MC1R gene could affect coat color but not black traits. There would be merit in further studies using molecular techniques to elucidate the cause of black traits in these Black-boned sheep.     

Extraction of RNA from tissues containing high levels of procyanidins that bind RNA

Commonly used methods for extraction of RNA from plants are not effective for isolation of high quality RNA from the pigmented seed coats of soybeans that produce procyanidins (tannins) during seed coat development. We demonstrate a significant modification of the phenol-LiCl method that yields high quality RNA from a black seed coat variety. In this method, seed coat material was ground in a buffer containing a high concentration of bovine serum albumin (100 mg BSA/50 mg of lyophilized seed coats) to competitively inhibit proanthocyanidin binding. The presence of hydrated insoluble polyvinylpoly-pyrrolidone (PVPP) was also necessary to bind proanthocyanidins and remove them from solution. Proteinase K was added to digest the remaining BSA, and phenol extraction was used to remove both the proteins and small molecular weight complexes formed by BSA and proanthocyanidins. After LiCl and ethanol precipitations, the RNA quality was examined by UV absorbance spectra, gel electrophoresis, and hybridization. Using this method, good quality RNA can be extracted from pigmented seed coats of soybean varieties that are homozygous for the recessivei allele and also contain the dominantT gene that results in production of procyanidins in the seed coat. The method is also effective for tissues from other plant species that contain abundant polyphenolic compounds.     

Melanocortin 1 receptor variation in the domestic dog

The melanocortin 1 receptor (Mc1r) is encoded by the Extension locus in many different mammals, where a loss-of-function causes exclusive production of red/yellow pheomelanin, and a constitutively activating mutation causes exclusive production of black/brown eumelanin. In the domestic dog, breeds with a wild-type E allele, e.g., the Doberman, can produce either pigment type, whereas breeds with the e allele, e.g., the Golden Retriever, produce exclusively yellow pigment. However, a black coat color in the Newfoundland and similar breeds is thought to be caused by an unusual allele of Agouti, which encodes the physiologic ligand for the Mc1r. Here we report that the predicted dog Mc1r is 317 residues in length and 96% identical to the fox Mc1r. Comparison of the Doberman, Newfoundland, Black Labrador, Yellow Labrador, Flat-coated Retriever, Irish Setter, and Golden Retriever revealed six sequence variants, of which two, S90G and R306ter, partially correlated with a black/brown coat and red/yellow coat, respectively. R306ter was found in the Yellow Labrador, Golden Retriever, and Irish Setter; the latter two had identical haplotypes but differed from the Yellow Labrador at three positions other than R306ter. In a larger survey of 194 dogs and 19 breeds, R306ter and a red/yellow coat were completely concordant except for the Red Chow. These results indicate that the e allele is caused by a common Mc1r loss-of-function mutation that either reoccurred or was subject to gene conversion during recent evolutionary history, and suggest that the allelic and locus relationships for dog coat color genes may be more analogous to those found in other mammals than previously thought.     

Synthesis of Streptovitacin-C2 Isomers

(2R*,4S*,6S*,αS*)- and (2R,4R,6R,αS)-Streptovitacin-C₂ (STV-C₂) (1a and 1b) were synthesized by an aldol condensation of (2R*,4S*)- or (2R,4R)-2,4-dimethyl-2-trimethylsiloxy-1-cyclohexanone (15a or 15b) with 4-(2-oxoethyl)-2,6-piperidinedione (16), which was followed by desilylation of the products. The stereochemistry of the synthesized STV-C₂ isomers (1a and 1b) was elucidated by NMR. STV-C₂ isomers (1a and 1b) did not show strong antimicrobial activity against Saccharomyces cerevisiae and Pyricularia oryzae.     

Variation of proline rich cell wall proteins in soybean lines with anthocyanin mutations

The I locus controls inhibition of anthocyanin accumulation in the epidermal cells of the soybean seed coat and affects abundance of PRP1, a proline-rich cell wall protein in the seed coat. Saline-soluble PRP1 is abundant in the developing seed coats of cultivar Richland (homozygous I, yellow), while it is significantly decreased in the pigmented isogenic mutant T157 (homozygous i, imperfect black). In this report, we examined soluble PRP1 in several cultivars containing alleles of the I locus which affect spatial distribution of pigmentation in the seed coat. We also characterized PRP1 in isolines with allelic variants of several other loci involved in seed coat pigmentation, including T and Im. The T gene is pleiotropic and affects both pubescence color and seed coat pigmentation and structure. Soluble PRP1 was abundant in the developing seed coats of lines with yellow seed (I or i ⁱ alleles) regardless of pubescence color, just as in Richland. Likewise, soluble PRP1 was decreased in pigmented seed coats (i ^k or i alleles) with grey (t) pubescence, as in T157. However, the total seed coat proteins were not extractable from pigmented seed coats with tawny pubescence (i, T genotypes) because they have proanthocyanidins that exhibit tannin properties. The dominant Im allele inhibits seed coat mottling (irregular patches of pigmentation) that occurs if plants are infected with soybean mosaic virus. PRP1 was 35 kDa in mottled (im) isolines and 34 kDa in non-mottled (Im) isolines. PRP2, which is expressed later in seed coat development and in the hypocotyl hooks of soybean seedlings, was also smaller in Im isolines. In summary, some of the anthocyanin mutations affect the quantity of soluble PRP1 polypeptides, while others correlate with structural changes in developmentally regulated proline-rich proteins.     

The role of the seed coat in adaptation of dimorphic seeds of the euhalophyte Suaeda salsa to salinity

The role of the seed coat in adaptation of dimorphic seeds of the euhalophyte Suaeda salsa to salinity was investigated during germination and early seedling growth. Black and brown seeds were treated with chloroform for 1 min before the extract was used to analyze waxes and the seeds to investigate the protective role of the seed coat under saline conditions. Waxes in black seed coats were more abundant than those in brown seed coats. Salinity (500 mM NaCl) increased the concentration of Na⁺ and decreased the concentration of K⁺ in both black and brown seeds regardless of chloroform treatment. Chloroform treatment alone (in the absence of NaCl) had no effect on the concentration of Na⁺ or K⁺ in black or brown seeds and in the presence of 500 mM NaCl had no effect on the concentration of Na⁺ or K⁺ in brown seeds. However, chloroform treatment increased Na⁺ and decreased K⁺ in black seeds with 500 mM NaCl. A change of MDA (malondialdehyde) concentration in black and brown seeds treated with or without chloroform was similar to the change of Na⁺ concentration. High salinity (1500 mM NaCl) pretreatment for 40 days had a less adverse effect on germination of black seeds compared with brown seeds after they were transferred to fresh water regardless of chloroform treatment. Similar results were found for seedling emergence. In conclusion, a black seed coat may be more protective than a brown seed coat, probably by shielding the embryo from ion toxicity, because of its higher content of waxes. Thus black seeds can better maintain seed viability than brown seeds for extended periods under hypersaline conditions.     

褐色种皮大豆与其黄色种皮衍生亲本的表型及基因型比较

大豆种皮色在从野生大豆到栽培大豆的选择过程中逐渐由黑色变成黄色,是重要的形态标记,因此,大豆种皮色相关基因的研究无论是对进化理论研究还是育种实践都具有非常重要的意义。利用褐色种皮J1265-2大豆及其衍生亲本黄色种皮大豆J1265-1为材料,通过SSR引物扩增片段,检验遗传背景的异同,同时对控制种皮的候选基因GmF3’H进行扩增和测序分析。结果表明,褐色种皮和黄色种皮材料不仅用161对SSR分子标记检测没有发现差异,其褐色种皮候选基因GmF3’H的编码区及起始密码子上游1465 bp序列也是一致的。因此,证明褐色种皮J1265-2大豆与其衍生亲本黄色种皮大豆J1265-1为近等基因系,其控制褐色种皮的基因型与已报道的基因型不同。     

藜异型性种子后代植株盐响应生理机制

种子异型性是植物适应异质生境的重要策略,异型性对后代植株的影响值得深入研究。以具有种子异型性的荒漠植物藜为材料,测定了异型种子后代植株在不同浓度(0,50,300 mmol/L)Na Cl胁迫下的表型及与耐盐相关的生理指标变化,探讨了异型种子后代植株之间对盐胁迫生理响应机制的差异。结果显示,褐色种子后代植株在各浓度盐胁迫下的表型(株高、分枝数)均优于黑色种子。对其生理指标测定结果显示,褐色种子植株除电导率显著低于黑色种子植株外,氧化损伤指标(氧自由基、丙二醛含量)及抗氧化酶(SOD、CAT、POX)活性、抗氧化剂(Car、As A)含量、渗调物质(可溶性糖、脯氨酸、甜菜碱)含量等在两者之间无明显差异。研究结果暗示,藜异型性种子后代植株的早期生长表型在盐胁迫下所产生的差异可能是由种子胚的大小及萌发快慢差异所导致,而这种差异并未引起盐胁迫下两种植株抗氧化系统响应的差异。     

Seed colour and post-fire bird predation in a Mediterranean pine forest

In a Pinus halepensis Mill. forest, a field experiment was designed to evaluate post-fire seed predation as affected by combinations of seed colour and soil substrates: light grey and black seeds combined with light grey ash, dark grey ash and pale brown sand. A survey of bird species inhabiting the area was also carried out and polyphenolic content of seed coat was assessed in seed lots of different colour. Light grey seeds were observed to be less predated on light grey ash, suggesting eucrypsis as a protective strategy against bird predation. On the contrary, no clear pattern was observed for the predation of black seeds on different substrates. In the study area both bird species breaking the seed coat and eating the endosperm and bird species swallowing the whole seed were monitored. We have estimated that more seeds were swallowed than broken, in all colour categories. Light grey seeds, which were found to have a higher content of polyphenols, were predated more than black seeds when exposed on the same substrate. Thus, no evidence was produced that the amount of polyphenols in seed coat could protect seeds from predation.     

Chalcone synthase mRNA and activity are reduced in yellow soybean seed coats with dominant I alleles.

The seed of all wild Glycine accessions have black or brown pigments because of the homozygous recessive i allele in combination with alleles at the R and T loci. In contrast, nearly all commercial soybean (Glycine max) varieties are yellow due to the presence of a dominant allele of the I locus (either I or i) that inhibits pigmentation in the seed coats. Spontaneous mutations to the recessive i allele occur in these varieties and result in pigmented seed coats. We have isolated a clone for a soybean dihydroflavonol reductase (DFR) gene using polymerase chain reaction. We examined expression of DFR and two other genes of the flavonoid pathway during soybean seed coat development in a series of near-isogenic isolines that vary in pigmentation as specified by combinations of alleles of the I, R, and T loci. The expression of phenylalanine ammonia-lyase and DFR mRNAs was similar in all of the gene combinations at each stage of seed coat development. In contrast, chalcone synthase (CHS) mRNA was barely detectable at all stages of development in seed coats that carry the dominant I allele that results in yellow seed coats. CHS activity in yellow seed coats (I) was also 7- to 10-fold less than in the pigmented seed coats that have the homozygous recessive i allele. It appears that the dominant I allele results in reduction of CHS mRNA, leading to reduction of CHS activity as the basis for inhibition of anthocyanin and proanthocyanin synthesis in soybean seed coats. A further connection between CHS and the I locus is indicated by the occurrence of multiple restriction site polymorphisms in genomic DNA blots of the CHS gene family in near-isogenic lines containing alleles of the I locus.     

Near isogenic lines of soybeans as tools to identify nodulation specificmutants of Bradyrhizobium elkanii

The dominant allele Rj4 in soybean interdicts or restricts the nodulation of plants by certain strains of bacteria, most of which are classified as Bradyrhizobium elkanii, while the recessive allele permits normal nodulation with the same strains. The near isogenic lines BARC-2 (Rj4) and BARC-3 (rj4) are calculated to be 99.95% identical in their nuclear DNA, but differ specifically in the allele present at the Rj4 locus. These lines were used to identify spontaneous mutants of the Rj4-restricted Bradyrhizobium elkanii strain USDA 61 Nal^r that had the ability to effectively nodulate plants of the Rj4 genotype. Of the eight rare nodules found on roots of soybean plants of the Rj4 genotype inoculated with the genetically marked strain USDA 61 Nal^r, four were identified as containing mutants with the ability to overcome the effects of the Rj4 allele.     

The brown coat colour of Coppernecked goats is associated with a non‐synonymous variant at the TYRP1 locus on chromosome 8

The recent development of a goat SNP genotyping microarray enables genome‐wide association studies in this important livestock species. We investigated the genetic basis of the black and brown coat colour in Valais Blacknecked and Coppernecked goats. A genome‐wide association analysis using goat SNP50 BeadChip genotypes of 22 cases and 23 controls allowed us to map the locus for the brown coat colour to goat chromosome 8. The TYRP1 gene is located within the associated chromosomal region, and TYRP1 variants cause similar coat colour phenotypes in different species. We thus considered TYRP1 as a strong positional and functional candidate. We resequenced the caprine TYRP1 gene by Sanger and Illumina sequencing and identified two non‐synonymous variants, p.Ile478Thr and p.Gly496Asp, that might have a functional impact on the TYRP1 protein. However, based on the obtained pedigree and genotype data, the brown coat colour in these goats is not due to a single recessive loss‐of‐function allele. Surprisingly, the genotype distribution and the pedigree data suggest that the ⁴⁹⁶Asp allele might possibly act in a dominant manner. The ⁴⁹⁶Asp allele was present in 77 of 81 investigated Coppernecked goats and did not occur in black goats. This strongly suggests heterogeneity underlying the brown coat colour in Coppernecked goats. Functional experiments or targeted matings will be required to verify the unexpected preliminary findings.     

Mutations in ASIP and MC1R: dominant black and recessive black alleles segregate in native Swedish sheep populations

By studying genes associated with coat colour, we can understand the role of these genes in pigmentation but also gain insight into selection history. North European short‐tailed sheep, including Swedish breeds, have variation in their coat colour, making them good models to expand current knowledge of mutations associated with coat colour in sheep. We studied ASIP and MC1R, two genes with known roles in pigmentation, and their association with black coat colour. We did this by sequencing the coding regions of ASIP in 149 animals and MC1R in 129 animals from seven native Swedish sheep breeds in individuals with black, white or grey fleece. Previously known mutations in ASIP [recessive black allele: g.100_105del (D₅) and/or g.5172T>A] were associated with black coat colour in Klövsjö and Roslag sheep breeds and mutations in both ASIP and MC1R (dominant black allele: c.218T>A and/or c.361G>A) were associated with black coat colour in Swedish Finewool. In Gotland, Gute, Värmland and Helsinge sheep breeds, coat colour inheritance was more complex: only 11 of 16 individuals with black fleece had genotypes that could explain their black colour. These breeds have grey individuals in their populations, and grey is believed to be a result of mutations and allelic copy number variation within the ASIP duplication, which could be a possible explanation for the lack of a clear inheritance pattern in these breeds. Finally, we found a novel missense mutation in MC1R (c.452G>A) in Gotland, Gute and Värmland sheep and evidence of a duplication of MC1R in Gotland sheep.     

Effects of salinity and nitrate on production and germination of dimorphic seeds applied both through the mother plant and exogenously during germination in Suaeda salsa

Salinity and nitrogen are two important environmental factors that affect the distribution of halophytes in their natural saline habitats. Seeds of the euhalophyte Suaeda salsa L. were harvested from plants that had been treated with 1 or 500 mm NaCl combined with 0.5 or 5 mm NO₃^?‐N (nitrate) for 115 days in a glasshouse. Germination was evaluated under different concentrations of NaCl and nitrate. Plants exposed to high salinity (500 mm ) and low nitrate (0.5 mm ) tended to produce heavy seeds. Either high salinity (500 mm ) or high nitrate (5 mm ) increased the brown/black seed ratio. The concentrations of Na⁺, K⁺, and Cl^? were higher in brown than in black seeds, and NO₃^? concentrations were higher in black than in brown seeds, regardless of NaCl and nitrate treatments during plant culture. Regardless of NaCl and nitrate concentrations during germination, seeds from plants grown with 0.5 mm nitrate generally germinated more rapidly than seeds from plants grown with 5 mm nitrate, and the difference was greater for black than for brown seeds. Exogenous nitrate during germination enhanced the germination of brown seeds less than that of black seeds. Producing more brown seeds and heavy black or brown seeds appears to be an adaptation of S. suaeda to saline environments. Producing more black seeds, which tend to remain dormant, should reduce competition for nitrogen and appears to be an adaptation to nitrogen‐limited environments. In conclusion, nitrate provided exogenously or by mother plants to black seeds may act as a signal molecule that enhances the germination of black S. suaeda seeds.     

EPR imaging and HPLC characterization of the pigment-based organic free radical in black soybean seeds

We investigated the location and distribution of paramagnetic species in dry black, brown, and yellow (normal) soybean seeds using electron paramagnetic resonance (EPR), X-band (9?GHz) EPR imaging (EPRI), and HPLC. EPR primarily detected two paramagnetic species in black soybean. These two different radical species were assigned as stable organic radical and Mn^2+?species based on the g values and hyperfine structures. The signal from the stable radical was noted at g?≈?2.00 and was relatively strong and stable. Subsequent noninvasive two-dimensional (2D) EPRI of the radical present in black soybean revealed that the stable radical was primarily located in the pigmented region of the soybean coat, with very few radicals observed in the soybean cotyledon (interior). Pigments extracted from black soybean were analyzed using HPLC. The major compound was found to be cyanidin-3-glucoside. Multi-EPR and HPLC results indicate that the stable radical was only found within the pigmented region of the soybean coat, and it could be cyanidin-3-glucoside or an oxidative decomposition product.     

Microsatellite mapping of the bovine roan locus: A major determinant of White Heifer Disease

In the Belgian Blue Cattle breed, coat color variation is mainly under the influence of a single autosomal locus, the roan locus, characterized by a pair of codominant alleles: r ⁺ (black) and R (white). Heterozygous r ⁺ R animals have intermingled black and white hairs, yielding the ``blue' phenotype typical of the breed. Major interest for the roan locus stems from its pleiotropic effect on fertility, owing to the critical role of the R allele in the determinism of White Heifer Disease. We describe the linkage mapping of the roan locus to bovine Chromosome (Chr) 5, in the interval between microsatellite markers BPI and AGLA293, with an associated lodscore of 11.2. Moreover, we map a candidate gene, the Steel locus coding for the mast cell growth factor, to bovine Chr 5. Received: 30 May 1995 / Accepted: 6 September 1995     

Characterization of tt15, a novel transparent testa mutant of Arabidopsis thaliana (L.) Heynh.

The Arabidopsis thaliana seed coat typically has a brown color due to the accumulation of flavonoid pigments in the testa. Mutants of A. thaliana with defects in pigment biosynthesis often produce seeds that are olive brown or even yellow in appearence, and the responsible genetic loci are referred to as TRANSPARENT TESTA (TT). Large-scale screening for mutants affected in seed development and complementation analysis of a candidate mutant line with all published A. thalianatt mutants identified a new tt locus designated tt15. The tt15 mutation maps to the lower part of chromosome 1. Mutant plants produced pale greenish-brown seeds whose dormancy was slightly reduced. The phenotype was consistent with the maternal origin of the testa. Analysis of pigment accumulation and the study of expression patterns of genes involved in flavonoid biosynthesis in tt15 plants and seeds indicated a seed-specific phenotype. Most notable was a reduction of the cyanidin and quercetin content of tt15 seeds. Received: 2 October 1998 / Accepted: 10 October 1998