Dataset Information

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method.

ABSTRACT: Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |?(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the 'Mantianhong' and 'Hongxiangsu' red-skinned cultivars. The 'Dangshansuli' cultivar genome was used as reference for sequence alignment. An average single-nucleotide polymorphism (SNP) index was calculated using a sliding window approach (200-kb windows, 20-kb increments). Nine scaffolds within the candidate QTL interval were in the fifth linkage group from 111.9 to 177.1?cM. There was a significant linkage between the insertions/deletions and simple sequence repeat markers designed from the candidate intervals and the red/green skin (R/G) locus, which was in a 582.5-kb candidate interval that contained 81 predicted protein-coding gene models and was composed of two subintervals at the bottom of the fifth chromosome. The ZFRI 130-16, In2130-12 and In2130-16 markers located near the R/G locus could potentially be used to identify the red skin trait in Asian pear populations. This study provides new insights into the genetics controlling the red skin phenotype in this fruit.

SUBMITTER: Xue H

PROVIDER: S-EPMC5674137 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method.

Xue Huabai H Shi Ting T Wang Fangfang F Zhou Huangkai H Yang Jian J Wang Long L Wang Suke S Su Yanli Y Zhang Zhen Z Qiao Yushan Y Li Xiugen X

Horticulture research 20171004

Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. T ...[more]

PMID: 29118994

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Project description:Anthocyanin concentration is the key determinant for red skin color in pear fruit. However, the molecular basis for development of red skin is complicated and has not been well-understood thus far. "Starkrimson" (Pyrus communis L.), an introduced red pear cultivated in the north of China and its green mutant provides a desirable red/green pair for identification of candidate genes involved in color variation. Here, we sequenced and annotated the transcriptome for the red/green color mutant at three stages of development using Illumina RNA-seq technology. The total number of mapped reads ranged from 26 to 46 million in six libraries. About 70.11-71.95% of clean reads could be mapped to the reference genome. Compared with green colored fruit, a total of 2230 differentially expressed genes (DEGs) were identified in red fruit. Gene Ontology (GO) terms were defined for 4886 differential transcripts involved in 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Three DEGs were identified as candidate genes in the flavonoid pathway, LAR, ANR, and C3H. Tellingly, higher expression was found for genes encoding ANR and LAR in the green color mutant, promoting the proanthocyanidin (PA) pathway and leading to lower anthocyanin. MYB-binding cis-motifs were identified in the promoter region of LAR and ANR. Based on these findings, we speculate that the regulation of PA biosynthesis might be a key factor for this red/green color mutant. Besides the known MYB and MADS transcription families, two new families, AP2 and WRKY, were identified as having high correlation with anthocyanin biosynthesis in red skinned pear. In addition, qRT-PCR was used to confirm the transcriptome results for 17 DEGs, high correlation of gene expression, further proved that AP2 and WARK regulated the anthocyanin biosynthesis in red skinned "Starkrimson," and ANR and LAR promote PA biosynthesis and contribute to the green skinned variant. This study can serve as a valuable new resource laying a solid foundation for functional gene identification in the anthocyanin pathway of red-skinned pear and provide a good reference for relevant research on molecular mechanisms of color variation in other pear species.

Project description:It is estimated that inherited red-green color deficiency, which involves both the protan and deutan deficiency types, is common in men. For red-green defective observers, some reddish colors appear desaturated and brownish, unlike those seen by normal observers. Despite its prevalence, few studies have investigated the effects that red-green color deficiency has on the psychological properties of colors (color emotions). The current study investigated the influence of red-green color deficiency on the following six color emotions: cleanliness, freshness, hardness, preference, warmth, and weight. Specifically, this study aimed to: (1) reveal differences between normal and red-green defective observers in rating patterns of six color emotions; (2) examine differences in color emotions related to the three cardinal channels in human color vision; and (3) explore relationships between color emotions and color naming behavior. Thirteen men and 10 women with normal vision and 13 men who were red-green defective performed both a color naming task and an emotion rating task with 32 colors from the Berkeley Color Project (BCP). Results revealed noticeable differences in the cleanliness and hardness ratings between the normal vision observers, particularly in women, and red-green defective observers, which appeared mainly for colors in the orange to cyan range, and in the preference and warmth ratings for colors with cyan and purple hues. Similarly, naming errors also mainly occurred in the cyan colors. A regression analysis that included the three cone-contrasts (i.e., red-green, blue-yellow, and luminance) as predictors significantly accounted for variability in color emotion ratings for the red-green defective observers as much as the normal individuals. Expressly, for warmth ratings, the weight of the red-green opponent channel was significantly lower in color defective observers than in normal participants. In addition, the analyses for individual warmth ratings in the red-green defective group revealed that luminance cone-contrast was a significant predictor in most red-green-defective individuals. Together, these results suggest that red-green defective observers tend to rely on the blue-yellow channel and luminance to compensate for the weak sensitivity of long- and medium-wavelength (L-M) cone-contrasts, when rating color warmth.

Dataset Information

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method.

Publications

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method.

Similar Datasets

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