Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits

Paes, Geísa Pinheiro; Viana, José Marcelo Soriano; Silva, Fabyano Fonseca e; Mundim, Gabriel Borges

doi:10.1590/1678-4685-gmb-2015-0126

Cited by 12 publications

(11 citation statements)

References 42 publications

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“…The LD of Chr 3 and 7 decayed faster than the other chromosomes, with~2.2 kb for a cut-off value of r 2 = 0.11. Past studies have found that this LD pattern (i.e., rapid decay with increasing physical distance) is typical in tropical maize germplasms [6,9,32]. The LD decay pattern in this study was similar to the findings of Yan et al [33] and Coan et al [6], who reported that the LD pattern (in tropical maize germplasms) decreases rapidly in the range of 0.1-10 kb.…”

Section: Linkage Disequilibriumsupporting

confidence: 90%

SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Maize with Network-Assisted Gene Prioritization

et al. 2019

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Maize (Zea mays L.) is one of the most crucial crops for global food security worldwide. For this reason, many efforts have been undertaken to address the efficient utilization of germplasm collections. In this study, 322 inbred lines were used to link genotypic variations (53,403 haplotype blocks (HBs) and 290,973 single nucleotide polymorphisms (SNPs)) to corresponding differences in flowering-related traits in two locations in Southern Brazil. Additionally, network-assisted gene prioritization (NAGP) was applied in order to better understand the genetic basis of flowering-related traits in tropical maize. According to the results, the linkage disequilibrium (LD) decayed rapidly within 3 kb, with a cut-off value of r2 = 0.11. Total values of 45 and 44 marker-trait associations (SNPs and HBs, respectively) were identified. Another important finding was the identification of HBs, explaining more than 10% of the total variation. NAGP identified 44, 22, and 34 genes that are related to female/male flowering time and anthesis-silking interval, respectively. The co-functional network approach identified four genes directly related to female flowering time (p < 0.0001): GRMZM2G013398, GRMZM2G021614, GRMZM2G152689, and GRMZM2G117057. NAGP provided new insights into the genetic architecture and mechanisms underlying flowering-related traits in tropical maize.

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Section: Linkage Disequilibriumsupporting

confidence: 90%

SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Maize with Network-Assisted Gene Prioritization

et al. 2019

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“…Regardless of the uncertainty of their function, class II TPSs show strict developmental and tissue specific gene regulation, strong diurnal regulation, and sensitivity to a variety of abiotic stressors [ 39 , 74 , 77 ]. The maize ZmTPSII.3.3 gene was shown to associate with the kernel expansion trait in popcorn [ 78 ]. The class II TPS proteins 5, 6 and 7 from Arabidopsis were found to be phosphoproteins and bind to 14–3-3 proteins when phosphorylated at Ser22 and Thr49 [ 76 ].…”

Section: Discussionmentioning

confidence: 99%

The role of Tre6P and SnRK1 in maize early kernel development and events leading to stress-induced kernel abortion

Bledsoe¹,

Henry

Griffiths

et al. 2017

BMC Plant Biol

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BackgroundDrought stress during flowering is a major contributor to yield loss in maize. Genetic and biotechnological improvement in yield sustainability requires an understanding of the mechanisms underpinning yield loss. Sucrose starvation has been proposed as the cause for kernel abortion; however, potential targets for genetic improvement have not been identified. Field and greenhouse drought studies with maize are expensive and it can be difficult to reproduce results; therefore, an in vitro kernel culture method is presented as a proxy for drought stress occurring at the time of flowering in maize (3 days after pollination). This method is used to focus on the effects of drought on kernel metabolism, and the role of trehalose 6-phosphate (Tre6P) and the sucrose non-fermenting-1-related kinase (SnRK1) as potential regulators of this response.ResultsA precipitous drop in Tre6P is observed during the first two hours after removing the kernels from the plant, and the resulting changes in transcript abundance are indicative of an activation of SnRK1, and an immediate shift from anabolism to catabolism. Once Tre6P levels are depleted to below 1 nmol∙g−1 FW in the kernel, SnRK1 remained active throughout the 96 h experiment, regardless of the presence or absence of sucrose in the medium. Recovery on sucrose enriched medium results in the restoration of sucrose synthesis and glycolysis. Biosynthetic processes including the citric acid cycle and protein and starch synthesis are inhibited by excision, and do not recover even after the re-addition of sucrose. It is also observed that excision induces the transcription of the sugar transporters SUT1 and SWEET1, the sucrose hydrolyzing enzymes CELL WALL INVERTASE 2 (INCW2) and SUCROSE SYNTHASE 1 (SUSY1), the class II TREHALOSE PHOSPHATE SYNTHASES (TPS), TREHALASE (TRE), and TREHALOSE PHOSPHATE PHOSPHATASE (ZmTPPA.3), previously shown to enhance drought tolerance (Nuccio et al., Nat Biotechnol (October 2014):1–13, 2015).ConclusionsThe impact of kernel excision from the ear triggers a cascade of events starting with the precipitous drop in Tre6P levels. It is proposed that the removal of Tre6P suppression of SnRK1 activity results in transcription of putative SnRK1 target genes, and the metabolic transition from biosynthesis to catabolism. This highlights the importance of Tre6P in the metabolic response to starvation. We also present evidence that sugars can mediate the activation of SnRK1. The precipitous drop in Tre6P corresponds to a large increase in transcription of ZmTPPA.3, indicating that this specific enzyme may be responsible for the de-phosphorylation of Tre6P. The high levels of Tre6P in the immature embryo are likely important for preventing kernel abortion.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-1018-2) contains supplementary material, which is available to authorized users.

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“…Association studies have been successfully used to identify the genetic basis of quantitative traits, allowing not only the identification of quantitative trait loci (QTLs), but also the identification of candidate genes based on statistical significant differences between markers and phenotypes [3]. Single nucleotide polymorphism (SNP) markers contributed to expand the knowledge of the genetic structure and diversity of maize populations.…”

Section: Introductionmentioning

confidence: 99%

“…Association mapping was successfully applied in maize to identify genomic regions related to plant height [4], root development [10], resistance to Fusarium graminearum Schwabe [11], and oil biosynthesis in maize kernels [9]. Mapping the associations of chromosomal regions of popcorn kernels revealed the candidate genes for starch, storage protein, pericarp polysaccharide, and oil grain contents in this maize variety [3]. However, little is known about the genes involved in the control of the main popcorn agronomic traits such as grain yield and popping expansion.…”

Section: Introductionmentioning

confidence: 99%

SNP-based mixed model association of growth- and yield-related traits in popcorn

Mafra¹,

Júnior²,

Filho³

et al. 2019

PLoS ONE

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The identification of the genes responsible for complex traits is highly promising to accelerate crop breeding, but such information is still limited for popcorn. Thus, in the present study, a mixed linear model-based association analysis (MLMA) was applied for six important popcorn traits: plant and ear height, 100-grain weight, popping expansion, grain yield and expanded popcorn volume per hectare. To this end, 196 plants of the open-pollinated popcorn population UENF-14 were sampled, selfed (S 1 ), and then genotyped with a panel of 10,507 single nucleotide polymorphisms (SNPs) markers distributed throughout the genome. The six traits were studied under two environments [Campos dos Goytacazes-RJ (ENV1) and Itaocara-RJ (ENV2)] in an incomplete block design. Based on the phenotypic data of the S 1 progenies and on the genetic characteristics of the parents, the MLMA was performed. Thereafter, genes annotated in the MaizeGDB platform were screened for potential linkage disequilibrium with the SNPs associated to the six evaluated traits. Overall, seven and eight genes were identified as associated with the traits in ENV1 and ENV2, respectively, and proteins encoded by these genes were evaluated for their function. The results obtained here contribute to increase knowledge on the genetic architecture of the six evaluated traits and might be used for marker-assisted selection in breeding programs.

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Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits

Cited by 12 publications

References 42 publications

SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Maize with Network-Assisted Gene Prioritization

SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Maize with Network-Assisted Gene Prioritization

The role of Tre6P and SnRK1 in maize early kernel development and events leading to stress-induced kernel abortion

SNP-based mixed model association of growth- and yield-related traits in popcorn

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