scholarly journals Explore the genetics of weedy traits using rice 3K database

2021 ◽  
Vol 62 (1) ◽  
Author(s):  
Yu-Lan Lin ◽  
Dong-Hong Wu ◽  
Cheng-Chieh Wu ◽  
Yung-Fen Huang
Keyword(s):  
Seed Coat ◽  
Coat Color ◽  
Rice Genome ◽  
Genome Project ◽  
Weedy Rice ◽  
Seed Coat Color ◽  
Allele Mining ◽  
Cultivated Rice ◽  
Population Structure Analysis ◽  
Public Data

Abstract Background Weedy rice, a conspecific weedy counterpart of the cultivated rice (Oryza sativa L.), has been problematic in rice-production area worldwide. Although we started to know about the origin of some weedy traits for some rice-growing regions, an overall assessment of weedy trait-related loci was not yet available. On the other hand, the advances in sequencing technologies, together with community efforts, have made publicly available a large amount of genomic data. Given the availability of public data and the need of “weedy” allele mining for a better management of weedy rice, the objective of the present study was to explore the genetic architecture of weedy traits based on publicly available data, mainly from the 3000 Rice Genome Project (3K-RGP). Results Based on the results of population structure analysis, we have selected 1378 individuals from four sub-populations (aus, indica, temperate japonica, tropical japonica) without admixed genomic composition for genome-wide association analysis (GWAS). Five traits were investigated: awn color, seed shattering, seed threshability, seed coat color, and seedling height. GWAS was conducted for each sub-population × trait combination and we have identified 66 population-specific trait-associated SNPs. Eleven significant SNPs fell into an annotated gene and four other SNPs were close to a putative candidate gene (± 25 kb). SNPs located in or close to Rc were particularly predictive of the occurrence of seed coat color and our results showed that different sub-populations required different SNPs for a better seed coat color prediction. We compared the data of 3K-RGP to a publicly available weedy rice dataset. The profile of allele frequency, phenotype-genotype segregation of target SNP, as well as GWAS results for the presence and absence of awns diverged between the two sets of data. Conclusions The genotype of trait-associated SNPs identified in this study, especially those located in or close to Rc, can be developed to diagnostic SNPs to trace the origin of weedy trait occurred in the field. The difference of results from the two publicly available datasets used in this study emphasized the importance of laboratory experiments to confirm the allele mining results based on publicly available data.

scholarly journals Genetic Mapping and Identification of the Candidate Gene for White Seed Coat in Cucurbita maxima

2021 ◽  
Vol 22 (6) ◽  
pp. 2972
Author(s):  
Yuzi Shi ◽  
Meng Zhang ◽  
Qin Shu ◽  
Wei Ma ◽  
Tingzhen Sun ◽  
...  
Keyword(s):  
Seed Coat ◽  
Molecular Breeding ◽  
Coat Color ◽  
Recessive Gene ◽  
Myb Transcription Factor ◽  
Cucurbita Maxima ◽  
Seed Coat Color ◽  
Rna Seq ◽  
Edible Seed ◽  
Segregating Population

Seed coat color is an important agronomic trait of edible seed pumpkin in Cucurbita maxima. In this study, the development pattern of seed coat was detected in yellow and white seed coat accessions Wuminglv and Agol. Genetic analysis suggested that a single recessive gene white seed coat (wsc) is involved in seed coat color regulation in Cucurbita maxima. An F2 segregating population including 2798 plants was used for fine mapping and a candidate region containing nine genes was identified. Analysis of 54 inbred accessions revealed four main Insertion/Deletion sites in the promoter of CmaCh15G005270 encoding an MYB transcription factor were co-segregated with the phenotype of seed coat color. RNA-seq analysis and qRT-PCR revealed that some genes involved in phenylpropanoid/flavonoid metabolism pathway displayed remarkable distinction in Wuminglv and Agol during the seed coat development. The flanking InDel marker S1548 was developed to predict the seed coat color in the MAS breeding with an accuracy of 100%. The results may provide valuable information for further studies in seed coat color formation and structure development in Cucurbitaceae crops and help the molecular breeding of Cucurbita maxima.

Harvest Loss and Seed Bank Longevity of Flax (Linum usitatissimum) Implications for Seed-Mediated Gene Flow

Weed Science ◽  
2011 ◽  
Vol 59 (1) ◽  
pp. 61-67 ◽  
Author(s):  
Jody E. Dexter ◽  
Amit J. Jhala ◽  
Rong-Cai Yang ◽  
Melissa J. Hills ◽  
Randall J. Weselake ◽  
...  
Keyword(s):  
Gene Flow ◽  
Seed Coat ◽  
Seed Bank ◽  
Coat Color ◽  
Oilseed Crop ◽  
Seed Coat Color ◽  
Flax Seed ◽  
Seed Loss ◽  
Artificial Seed ◽  
Seed Mediated

Flax is a minor oilseed crop in Canada largely exported to the European Union for use as a source of industrial oil and feed ingredient. While flax could be genetically engineered (GE) to enhance nutritional value, the adoption of transgenic technologies threatens conventional flax market acceptability. Harvest seed loss of GE crops and the persistence of GE crop volunteers in the seed bank are major factors influencing transgene persistence. Ten commercial fields in Alberta, Canada, were sampled after harvesting conventional flax in 2006 and 2007, and flax seed density and viability were determined. Additionally, artificial seed banks were established at two locations in Alberta in 2005 and 2006 to quantify persistence of five conventional flax cultivars with variability in seed coat color (yellow or brown) and α-linolenic acid (ALA, 18:3cisΔ9,13,15) content (3 to 55%) at three soil depths (0, 3, or 10 cm). Harvest methods influenced seed loss and distribution, > 10-fold more seed was distributed beneath windrows than between them. Direct harvested fields had more uniform seed distribution but generally higher seed losses. The maximum yield loss was 44 kg ha−1or 2.3% of the estimated crop yield. Seed loss and the viability of flax seed were significantly influenced by year, presumably because weather conditions prior to harvest influenced the timing and type of harvest operations. In artificial seed bank studies, seed coat color or ALA content did not influence persistence. Flax seed viability rapidly declined in the year following burial with < 1% remaining midsummer in the year following burial but there were significant differences between years. In three of four locations, there was a trend of longer seed persistence at the deepest burial depth (10 cm). The current study predicts that seed-mediated gene flow may be a significant factor in transgene persistence and a source of adventitious presence.

Map-based cloning and characterization of a gene controlling hairiness and seed coat color traits in Brassica rapa

2008 ◽  
Vol 69 (5) ◽  
pp. 553-563 ◽  
Author(s):  
Jiefu Zhang ◽  
Ying Lu ◽  
Yuxiang Yuan ◽  
Xiaowei Zhang ◽  
Jianfeng Geng ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Seed Coat ◽  
Coat Color ◽  
Seed Coat Color ◽  
Color Traits

scholarly journals Influence of Seed Coat Color Genes on Milling Qualities of Red Lentil (Lens culinaris Medik.)

2018 ◽  
Vol 10 (10) ◽  
pp. 88 ◽  
Author(s):  
Maya Subedi ◽  
Lope G. Tabil ◽  
Albert Vandenberg
Keyword(s):  
Seed Coat ◽  
Coat Color ◽  
Seed Coat Color ◽  
Milling Quality ◽  
Economic Trait ◽  
Milling Characteristics ◽  
Genotype Interaction ◽  
Dehulling Efficiency ◽  
Seed Characteristics ◽  
Seed Coats

Efficient milling is the key economic trait for the red lentil industry. Various seed characteristics including seed coat color can influence milling characteristics. Four basic seed coat ground colors (green, gray, tan, and brown) of 16 red lentil genotypes from a common genetic background were compared to determine the effect of seed coat color genes on three key milling quality traits: dehulling efficiency (DE), milling recovery (MR), and football recovery (FR). These genotypes were grown at two locations in Saskatchewan, Canada for two years. DE, MR, and FR results varied depending on the seed coat color conferred by specific genotypes. Green and gray seed coat color (homozygous recessive tgc allele) genotypes had significantly higher DE and MR percentages compared to brown or tan seed coat types (homozygous dominant Tgc allele) depending on genotype interaction with site-year. Seeds with brown or tan seed coats had significantly higher FR percentages in two site-years. Red cotyledon lentils with uniform shape and green or gray seed coat color might be more profitable for millers who wish to maximize DE and MR of red lentil, but brown seed coat color might be preferable in terms of FR.

scholarly journals Mapping and identification of yellow seed coat color genes in Brassica juncea L.

2020 ◽  
Author(s):  
Zhen Huang ◽  
Yang Wang ◽  
Hong Lu ◽  
Xiang Liu ◽  
Lu Liu ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Brassica Juncea ◽  
Seed Coat ◽  
Coat Color ◽  
Seed Color ◽  
Seed Coat Color ◽  
Flavonoid Pathway ◽  
Yellow Seed ◽  
Color Formation ◽  
Yellow Seed Coat

Abstract BackgroundYellow seed breeding is an effective method to improve the oil content in rapeseed. Yellow seed coat color formation is influenced by various factors, and no clear mechanisms are known. In this study, Bulked segregant RNA-Seq (BSR-Seq) of BC9 population of Wuqi mustard (yellow seed) and Wugong mustard (brown seed) was used to identity the candidate genes controlling the yellow seed color in Brassica juncea L.ResultsYellow seed coat color gene was mapped to chromosome A09, and differentially expressed genes (DEGs) between brown and yellow bulks enriched in the flavonoid pathway. A significant correlation between the expression of BjF3H and BjTT5 and the content of the seed coat color related indexes was identified. Two intron polymorphism (IP) markers linked to the target gene were developed around BjF3H. Therefore, BjF3H was considered as the candidate gene. The BjF3H coding sequences (CDS) of Wuqi mustard and Wugong mustard are 1071-1077bp, encoding protein of 356-358 amino acids. One amino acid change (254, F/V) was identified in the conserved domain. This mutation site was detected in four Brassica rapa (B. rapa) and six Brassica juncea (B. juncea) lines, but not in Brassica napus (B. napus).ConclusionsThe results indicated BjF3H is a candidate gene that related to yellow seed coat color formation in Brassica juncea and provided a comprehensive understanding of the yellow seed coat color mechanism.

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