Construction of a high-density genetic map: genotyping by sequencing (GBS) to map purple seed coat color (Psc) in hulless barley

Abstract Background Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. Results The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. Conclusions This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.

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Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map

BMC Genomics ◽

10.1186/s12864-015-2316-4 ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 40

Author(s):

Linhai Wang ◽

Qiuju Xia ◽

Yanxin Zhang ◽

Xiaodong Zhu ◽

Xiaofeng Zhu ◽

...

Keyword(s):

Plant Height ◽

Genetic Map ◽

Fine Mapping ◽

Seed Coat ◽

Genome Assembly ◽

Coat Color ◽

High Density ◽

Seed Coat Color

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Further Studies on the Effect of Seed Coat Color on Agronomic and Chemical Characters and Seed Injury in Flax 1

Agronomy Journal ◽

10.2134/agronj1960.00021962005200040010x ◽

1960 ◽

Vol 52 (4) ◽

pp. 210-212 ◽

Cited By ~ 5

Author(s):

J. O. Culbertson ◽

V. E. Comstock ◽

R. A. Frederiksen

Keyword(s):

Seed Coat ◽

Coat Color ◽

Seed Coat Color ◽

Chemical Characters

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

International Journal of Molecular Sciences ◽

10.3390/ijms22062972 ◽

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.

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Explore the genetics of weedy traits using rice 3K database

Botanical Studies ◽

10.1186/s40529-020-00309-y ◽

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.

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Location of Genes for Seed Coat Color in Hexaploid Wheat, Triticum aestivum L. 1

Crop Science ◽

10.2135/cropsci1970.0011183x001000050012x ◽

1970 ◽

Vol 10 (5) ◽

pp. 495-496 ◽

Cited By ~ 36

Author(s):

R. J. Metzger ◽

B. A. Silbaugh

Keyword(s):

Triticum Aestivum ◽

Seed Coat ◽

Hexaploid Wheat ◽

Coat Color ◽

Triticum Aestivum L ◽

Seed Coat Color

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

Weed Science ◽

10.1614/ws-d-10-00047.1 ◽

2011 ◽

Vol 59 (1) ◽

pp. 61-67 ◽

Cited By ~ 5

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.

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