A High-Density Genetic Map Identifies a Novel Major QTL for Boron Efficiency in Oilseed Rape (Brassica napus L.)

Zhang, Didi; Hua, Yingpeng; Wang, Xiaohua; Zhao, Hua; Shi, Lei; Xu, Fangsen

doi:10.1371/journal.pone.0112089

Cited by 50 publications

(62 citation statements)

References 49 publications

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“…Moreover, many traits of agronomic importance in B. napus , such as seed coat color, oil content, and seed yield, are quantitative with complex genetic bases. Recently, a high-density linkage map was constructed using the Brassica 60 K Infinium BeadChip Array (Zou et al, 2012; Delourme et al, 2013; Liu et al, 2013; Zhang et al, 2014; Wang et al, 2015). Genome-specific SSR markers have been widely used for genetic mapping, association mapping, comparative mapping, QTL analysis, and marker-assisted selection (Li et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus

Zhao

et al. 2016

Front. Plant Sci.

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Flavonoids are secondary metabolites that are extensively distributed in the plant kingdom and contribute to seed coat color formation in rapeseed. To decipher the genetic networks underlying flavonoid biosynthesis in rapeseed, we constructed a high-density genetic linkage map with 1089 polymorphic loci (including 464 SSR loci, 97 RAPD loci, 451 SRAP loci, and 75 IBP loci) using recombinant inbred lines (RILs). The map consists of 19 linkage groups and covers 2775 cM of the B. napus genome with an average distance of 2.54 cM between adjacent markers. We then performed expression quantitative trait locus (eQTL) analysis to detect transcript-level variation of 18 flavonoid biosynthesis pathway genes in the seeds of the 94 RILs. In total, 72 eQTLs were detected and found to be distributed among 15 different linkage groups that account for 4.11% to 52.70% of the phenotypic variance atrributed to each eQTL. Using a genetical genomics approach, four eQTL hotspots together harboring 28 eQTLs associated with 18 genes were found on chromosomes A03, A09, and C08 and had high levels of synteny with genome sequences of A. thaliana and Brassica species. Associated with the trans-eQTL hotspots on chromosomes A03, A09, and C08 were 5, 17, and 1 genes encoding transcription factors, suggesting that these genes have essential roles in the flavonoid biosynthesis pathway. Importantly, bZIP25, which is expressed specifically in seeds, MYC1, which controls flavonoid biosynthesis, and the R2R3-type gene MYB51, which is involved in the synthesis of secondary metabolites, were associated with the eQTL hotspots, and these genes might thus be involved in different flavonoid biosynthesis pathways in rapeseed. Hence, further studies of the functions of these genes will provide insight into the regulatory mechanism underlying flavonoid biosynthesis, and lay the foundation for elaborating the molecular mechanism of seed coat color formation in B. napus.

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Section: Discussionmentioning

confidence: 99%

Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus

Zhao

et al. 2016

Front. Plant Sci.

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“…Many other candidate genes were identified that are associated with the variation of number of pods per plants. Among the candidate genes, basic helixloop-helix (bHLH) DNA-binding superfamily protein that is involved in the development and dehiscence of seed and pod (Hudson and Hudson, 2015), protein kinase superfamily protein is involved in pollen abortion (Radchuk et al, 2006), pyruvate kinase family protein associated with early embryo abortion of flower (Zhang et al, 2014), ARM repeat superfamily protein is involved in self-incompatibility and reduction of pod number (Sharma and Pandey, 2016), chaperone DNAJ-domain superfamily protein is involved in male sterility (Yang et al, 2009), DNAJ heat shock Nterminal domain-containing protein that increases tolerance to heat and prevents fruit drop (Zhao et al, 2015), prolinerich family protein associated with flower and pod development (Giorno et al, 2013), adenine nucleotide alpha hydrolases-like superfamily protein is involved in male sterility (Mok and Mok, 2001), homeodomain-like protein regulates anther dehiscence (Wilson et al, 2011), cytochrome P450 is involved in the pollen tube development and fertilization (Zhao et al, 2015), pyruvate kinase family protein found associated with early embryo abortion (Zhang et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

“…Pod length is also affected by heat stress. High temperature reduces the photosynthetic capacity (CraftsBrandner and Salvucci, 2002) and increase pollen abortion (Zhang et al, 2014), which in turn affects the growth and development of pod. We have identified 11 QTL associated with pod length in relation to heat stress.…”

Section: Discussionmentioning

confidence: 99%

“…One marker, chrA03_4124353, located on chromosome A3, is only 1 kb away from Brassica gene BnaA03g09160D (Cysteine/Histidine-rich C1 domain family protein). This gene is involved in tapetal development, programmed cell death (PCD) and pollen grain sterility (Zhang et al, 2014). Many other genes such as 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein (Leisner et al, 2014), cysteine/histidine-rich C1 domain family protein (Zhang et al, 2014), heat shock protein 18.2 (Kim and Hong, 2001), zinc finger (C3HC4-type RING finger) family protein (Wu et al, 2014), cellulose synthase like A14 (Park et al, 2013), homeodomain-like superfamily protein (Wilson et al, 2011), syntaxin of plants 71 (Sharma and Nayyar, 2014), cellulose synthase 5 (Park et al, 2013), plant selfincompatibility protein S1 family (Samuel et al, 2009), cytochrome P450 (Zhao et al, 2015), ubiquitin family protein (Mazzucotelli et al, 2006), malectin/receptor-like protein kinase family protein (Matschi et al, 2013), glutamine synthetase 1;4 (Bargaz et al, 2015), auxin response factor 19 (Li et al, 2016), AGAMOUS-like 24 (Yu et al, 2002), P450 reductase 1 (Bak et al, 2011) were also identified associated with the cytoplasmic male sterility, pollen tube and pollen coat development, boron deficiency, and seed pod development.…”

Section: Discussionmentioning

confidence: 99%

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Association mapping of agronomic traits of canola (Brassica napus L.) subject to heat stress under field conditions

Rahaman¹,

Mamidi²,

Rahman³

2017

Aust J Crop Sci

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Brassica is a cool season crop and is susceptible to high temperatures. Developing heat stress tolerant varieties will help the crop to sustain under high temperature and can be used to extend the geographical range of cultivation. We have phenotyped 84 spring type Brassica napus accessions in field under natural heat conditions. Data on various agronomic traits were collected at the end of flowering to maturity stages. An association mapping study was performed to identify QTL associated with heat stress tolerant agronomic traits. A total of 37,269 single nucleotide polymorphism markers were used for this study. Multiple markers distributed on most of the chromosomes were identified. A total of 6, 11, 7, 11 and 7 QTL were identified those explained 52.2%, 71.8%, 53.2%, 73.5% and 61.0% of the total phenotypic variations for plant height, main raceme height, pods on main raceme, pod length, and sterile/aborted pod, respectively. Multiple candidate genes known to be involved in abiotic stress and abortion of different organs were identified in the vicinity of the QTL. For instance, B. napus BnaA03g09160D gene involved in programmed cell death and pollen sterility, BnaA05g33770D and BnaA05g33780D genes associated with pollen sterility and pod abortion were identified in the QTL regions.

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“…In order to improve quality and yield in crops, molecular markers have been widely used to study germplasm diversity [4,5]. To date, numerous molecular marker technologies continue to be developed and used in plant genetic analysis.…”

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confidence: 99%

Identification, evaluation, and application of the genomic-SSR loci in ramie

et al. 2016

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To provide a theoretical and practical foundation for ramie genetic analysis, simple sequence repeats (SSRs) were identified in the ramie genome and employed in this study. From the 115 369 sequences of a specific-locus amplified fragment library, a type of reduced representation library obtained by high-throughput sequencing, we identified 4774 sequences containing 5064 SSR motifs. SSRs of ramie included repeat motifs with lengths of 1 to 6 nucleotides, and the abundance of each motif type varied greatly. We found that mononucleotide, dinucleotide, and trinucleotide repeat motifs were the most prevalent (95.91%). A total of 98 distinct motif types were detected in the genomic-SSRs of ramie. Of them, The A/T mononucleotide motif was the most abundant, accounting for 41.45% of motifs, followed by AT/ TA, accounting for 20.30%. The number of alleles per locus in 31 polymorphic microsatellite loci ranged from 2 to 7, and observed and expected heterozygosities ranged from 0.04 to 1.00 and 0.04 to 0.83, respectively. Furthermore, molecular identity cards (IDs) of the germplasms were constructed employing the ID Analysis 3.0 software. In the current study, the 26 germplasms of ramie can be distinguished by a combination of five SSR primers including . The allele polymorphisms produced by all SSR primers were used to analyze genetic relationships among the germplasms. The similarity coefficients ranged from 0.41 to 0.88. We found that these 26 germplasms were clustered into five categories using UPGMA, with poor correlation between germplasm and geographical distribution. Our study is the first large-scale SSR identification from ramie genomic sequences. We have further studied the SSR distribution pattern in the ramie genome, and proposed that it is possible to develop SSR loci from genomic data for population genetics studies, linkage mapping, quantitative trait locus mapping, cultivar fingerprinting, and as genetic diversity studies.

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A High-Density Genetic Map Identifies a Novel Major QTL for Boron Efficiency in Oilseed Rape (Brassica napus L.)

Cited by 50 publications

References 49 publications

Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus

Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus

Association mapping of agronomic traits of canola (Brassica napus L.) subject to heat stress under field conditions

Identification, evaluation, and application of the genomic-SSR loci in ramie

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