QTL identification and meta-analysis for kernel composition traits across three generations in popcorn

Dong, Yuchen; Zhang, Zhongwei; Shi, Qingling; Wang, Qilei; Zhou, Qiang; Li, Yuling

doi:10.1007/s10681-015-1360-0

Cited by 16 publications

(27 citation statements)

References 39 publications

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“…It was expected that in the studied population (UENF-14) all loci were in HWE, as the selected individuals produced the plants that would then be recombined to form a subsequent improved population. However, of the 16 EST-SSR primers, only six loci showed HWE in all cycles; three of them (Umc1948, Umc1327, and Umc1389) were related to quantitative trait loci (QTL) in popcorn (Dong et al, 2015;Li et al, 2007). This confirms how the potential effect of genetic drift could increase the probability of eliminating certain genotypes and consequently contribute to the predominance of certain genotypic combinations in the population (Cruz et al, 2011;Souza Júnior et al, 2000).…”

Section: Discussionmentioning

confidence: 85%

“…Therefore, this study monitored the impact of nine selective cycles on the structure and genetic diversity of the UENF-14 popcorn population. Although the two main selection characteristics are productivity and grain expansion capacity in the population improvement program of the UENF-14 popcorn population, among the 16 EST-SSR primers it was detected that six are associated with important quantitative trait loci (QTL) for popcorn: two for popping expansion (Umc1948 and Umc1155) (Babu et al, 2006;Li, Dong, Niu, & Cui, 2007) and four for nutritional quality: Umc1196 is associated with oil content; Umc1389 with protein and starch content; Umc1327 with the amino acid lysine; and Umc1714 with protein content (Dong et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

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<b>Population structure and impact of recurrent selection on popcorn using EST-SSR markers

et al. 2018

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The success of any recurrent selection program depends on the genetic variability of the evaluated population, which is used to refer to the diversity of existing alleles at many genetic loci. Thus, the goal of the present study was to investigate the impact of recurrent selection across nine cycles of a UENF-14 popcorn population through the analysis of genetic diversity and structure using microsatellite markers (EST-SSRs). Genomic DNA was extracted from young leaves of 25 individuals from each cycle (C0, C1 C2, C3, C4, C5, C6, C7, and C8), totaling 225 samples from the UENF-14 population. Fifty EST-SSR markers were used for the analysis of genetic diversity across the recurrent selection cycles, 16 of which were polymorphic. Thirty-four alleles were detected, with an average of 2.13 alleles per locus. Throughout all the recurrent selection cycles, there was a reduction in heterozygosity and an increase in inbreeding. The population structure showed a sharing of alleles, inferring that some may be directly related to the main selection characteristics.

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Section: Discussionmentioning

confidence: 85%

Section: Discussionmentioning

confidence: 99%

<b>Population structure and impact of recurrent selection on popcorn using EST-SSR markers

et al. 2018

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“…The four SNPs identified in this study as associated with popping expansion are located in bins 2.03, 3.06, and 9.03 (Table 3). Although no QTLs for popping expansion QTLs in bin 3.06 have been reported previously, a meta‐QTL analysis performed by Dong et al (2015) highlighted the importance of the 2.03 and 9.03 genomic bins for popping expansion, starch content, and other related traits to popping quality. The relatively small number of genomic regions identified as associated with popping expansion compared with previous linkage‐based mapping studies (Li et al, 2007, 2008; Dong et al, 2012) is likely due to the limited power of GWAS to identify variants closely associated with population structure.…”

Section: Discussionmentioning

confidence: 98%

Genomic‐Wide Association Study of Popping Expansion in Tropical Popcorn and Field Corn Germplasm

Senhorinho¹,

Coan²,

Marino

et al. 2019

Crop Science

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Popcorn is a popular snack food with higher grain value compared with “field corn” maize (Zea mays L.). In general, popcorn germplasm is less improved than common maize cultivars, with less favorable agronomic performance and greater susceptibility to pests, diseases, and lodging, especially in tropical environments. One approach to expanding and improving popcorn germplasm is to introduce favorable alleles for agronomic performance from field corn. If markers tagging quantitative trait loci (QTLs) associated with popping expansion were identified, they could be selected with markers to maintain popping expansion in breeding populations derived from crosses between field and popcorn germplasm. The objectives of this study were to identify single nucleotide polymorphism (SNP) markers and putative candidate genes associated with higher popping expansion in a diverse sample of popcorn and field corns relevant to Brazilian breeding programs. We applied a comprehensive genome‐wide association study (GWAS) for popping expansion, using 165,089 SNP markers in 183 inbred lines with 2 yr of trial data. Four SNPs were significantly associated with popping expansion, three of which were colocalized to previously reported meta‐QTLs, and one that was novel. Annotated genes closely linked to the associated SNPs were identified with functions related with starch content, which plays an important role in popping expansion quality. If these associations can be validated independently, they can be useful for breeders to select agronomically superior genotypes with greater popping expansion.

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“…The QTL meta‐analysis approach was applied in this study, which not only improved the accuracy and validity of our QTL mapping but also provided a new method for revealing the consensus QTLs from a consensus genetic map by comparing different map positions. Using this method, a number of studies have reported QTL meta‐analysis using BioMercator software (Dong et al., ; Said et al., ; Shinozuka, Cogan, Spangenberg, & Forster, ; Swamy & Sarla, ), and a large number of candidate genes have been mined in these studies. In the present study, candidate genes were screened from consensus, homologous candidate genes that were mined using the blast tool (Table ): three heading date cloned genes, OsMADS34 (Lin et al., ), Se14 (Yokoo et al., ) and ehd2 (Matsubara et al., ), are homologous with four candidate genes; two chlorophyll content‐related cloned genes, OsRopGEF10 (Yoo et al., ) and Sll1 (Zhang et al., 2009a), are homologous with six candidate genes; two drought tolerance cloned genes sHSP17.7 (Sato & Yokoya, ) and OsDREB1E (Chen et al., ) are homologous with four candidate gene; and two cold tolerance cloned genes OsMYB2 (Yang et al., ) and MYBS3 (Su et al., ) are homologous with five candidate gene.…”

Section: Discussionmentioning

confidence: 99%

“…Using this method, a number of studies have reported QTL metaanalysis using BioMercator software (Dong et al, 2015;Said et al, 2015;Shinozuka, Cogan, Spangenberg, & Forster, 2012;Swamy & Sarla, 2011), and a large number of candidate genes have been mined in these studies. In the present study, candidate genes were screened from consensus, homologous candidate genes that were mined using the blast tool (Table 7): three heading date cloned genes, OsMADS34 (Lin et al, 2014), Se14 (Yokoo et al, 2014) and…”

Section: Meta-analysis Of Qtls and Identification Of Candidate Genesmentioning

confidence: 99%

QTL mapping for heading date, leaf area and chlorophyll content under cold and drought stress in two related recombinant inbred line populations (Japonica rice) and meta‐analysis

et al. 2018

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Rice is highly susceptible to drought and cold. The goal of this study was to identify the QTLs affecting the rice heading date (HD), leaf area (LA) and chlorophyll content (CC) under cold and drought stress. A total of twenty‐nine and thirty‐eight additive QTLs were detected from two crosses of ‘Dongnong422’/‘Kongyu131’ and ‘Xiaobaijingzi’/‘Kongyu131’, respectively. qHD1‐7‐1, qHD1‐7‐2, qHD1‐2‐1, qLA1‐7‐1, qLA1‐6‐3 and qCC1‐7‐1 show adaptive effects under cold treatment, while qHD2‐2‐3, qHD2‐2‐2, qLA2‐7‐3 and qCC2‐5‐1 were important for explaining the genetic mechanism during drought tolerance. Additionally, nine and five additive × environment interaction QTLs were detected for two RILs, respectively. RIL26 and RIL73 were two lines that are associated with cold and drought for HD. 339 QTLs related to HD, CC and LA of rice from database and our research were projected onto the genetic map. Nine cloned genes and nineteen homologous candidate genes related to HD, CC, cold tolerance and drought tolerance were mapped by meta‐analysis. These results lay the foundation for the fine mapping of QTLs related to HD, LA and CC for marker‐assisted selection.

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QTL identification and meta-analysis for kernel composition traits across three generations in popcorn

Cited by 16 publications

References 39 publications

<b>Population structure and impact of recurrent selection on popcorn using EST-SSR markers

<b>Population structure and impact of recurrent selection on popcorn using EST-SSR markers

Genomic‐Wide Association Study of Popping Expansion in Tropical Popcorn and Field Corn Germplasm

QTL mapping for heading date, leaf area and chlorophyll content under cold and drought stress in two related recombinant inbred line populations (Japonica rice) and meta‐analysis

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