Dataset Information

Stable QTLs for Plant Height on Chromosome A09 Identified From Two Mapping Populations in Peanut (Arachis hypogaea L.).

ABSTRACT: The peanut (Arachis hypogaea L.) is an important grain legume extensively cultivated worldwide, supplying edible oil and protein for human consumption. As in many other crops, plant height is a crucial factor in determining peanut architecture traits and has a unique effect on resistance to lodging and efficiency of mechanized harvesting as well as yield. Currently, the genetic basis underlying plant height remains unclear in peanut, which have hampered marker-assisted selection in breeding. In this study, we conducted a quantitative trait locus (QTL) analysis for peanut plant height by using two recombinant inbred line (RIL) populations including "Yuanza 9102 × Xuzhou 68-4 (YX)" and "Xuhua 13 × Zhonghua 6 (XZ)". In the YX population, 38 QTLs including 10 major QTLs from 9 chromosomes were detected in 4 environments, and 8 consensus QTLs integrated by meta-analysis expressed stably across multiple environments. In the XZ population, 3 major QTLs and seven minor QTLs from 6 chromosomes were detected across 3 environments. Generally, most major QTLs from the two populations were located on pseudomolecule chromosome 9 of Arachis duranesis (A09), indicating there would be key genes on A09 controlling plant height. Further analysis revealed that qPHA09.1a from the XZ population and one consensus QTL, cqPHA09.d from the YX population were co-localized in a reliable 3.4 Mb physical interval on A09, which harbored 161 genes including transcription factors and enzymes related to signaling transduction and cell wall formation. The major and stable QTLs identified in this study may be useful for further gene cloning and identification of molecular markers applicable for breeding.

SUBMITTER: Lv J

PROVIDER: S-EPMC5982159 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Stable QTLs for Plant Height on Chromosome A09 Identified From Two Mapping Populations in Peanut (<i>Arachis hypogaea</i> L.).

Lv Jianwei J Liu Nian N Guo Jianbin J Xu Zhijun Z Li Xinping X Li Zhendong Z Luo Huaiyong H Ren Xiaoping X Huang Li L Zhou Xiaojing X Chen Yuning Y Chen Weigang W Lei Yong Y Tu Jinxing J Jiang Huifang H Liao Boshou B

Frontiers in plant science 20180525

The peanut (<i>Arachis hypogaea</i> L.) is an important grain legume extensively cultivated worldwide, supplying edible oil and protein for human consumption. As in many other crops, plant height is a crucial factor in determining peanut architecture traits and has a unique effect on resistance to lodging and efficiency of mechanized harvesting as well as yield. Currently, the genetic basis underlying plant height remains unclear in peanut, which have hampered marker-assisted selection in breedi ...[more]

PMID: 29887872

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Project description:Bacterial wilt (BW) caused by Ralstonia solanacearum is a serious, global, disease of peanut (Arachis hypogaea L.), but it is especially destructive in China. Identification of DNA markers linked to the resistance to this disease will help peanut breeders efficiently develop resistant cultivars through molecular breeding. A F2 population, from a cross between disease-resistant and disease-susceptible cultivars, was used to detect quantitative trait loci (QTL) associated with the resistance to this disease in the cultivated peanut. Genome-wide SNPs were identified from restriction-site-associated DNA sequencing tags using next-generation DNA sequencing technology. SNPs linked to disease resistance were determined in two bulks of 30 resistant and 30 susceptible plants along with two parental plants using bulk segregant analysis. Polymorphic SSR and SNP markers were utilized for construction of a linkage map and for performing the QTL analysis, and a moderately dense linkage map was constructed in the F2 population. Two QTL (qBW-1 and qBW-2) detected for resistance to BW disease were located in the linkage groups LG1 and LG10 and account for 21 and 12 % of the bacterial wilt phenotypic variance. To confirm these QTL, the F8 RIL population with 223 plants was utilized for genotyping and phenotyping plants by year and location as compared to the F2 population. The QTL qBW-1 was consistent in the location of LG1 in the F8 population though the QTL qBW-2 could not be clarified due to fewer markers used and mapped in LG10. The QTL qBW-1, including four linked SNP markers and one SSR marker within 14.4-cM interval in the F8, was closely related to a disease resistance gene homolog and was considered as a candidate gene for resistance to BW. QTL identified in this study would be useful to conduct marker-assisted selection and may permit cloning of resistance genes. Our study shows that bulk segregant analysis of genome-wide SNPs is a useful approach to expedite the identification of genetic markers linked to disease resistance traits in the allotetraploidy species peanut.

Project description:BackgroundFatty acid composition of oil extracted from peanut (Arachis hypogaea L.) seed is an important quality trait because it may affect the flavor and shelf life of resulting food products. In particular, a high ratio of oleic (C18:1) relative to linoleic (C18:2) fatty acid (O/L ? 10) results in a longer shelf life. Previous reports suggest that the high oleic (~80%) trait was controlled by recessive alleles of ahFAD2A and ahFAD2B, the former of which is thought to have a high frequency in US runner- and virginia-type cultivars. Functional mutations, G448A in ahFAD2A and 442insA in ahFAD2B eliminate or knock down desaturase activity and have been demonstrated to produce peanut oil with high O/L ratios. In order to employ marker assisted selection (MAS) to select a high oleic disease resistant peanut and to evaluate genotypic and phenotypic variation, crosses were made between high oleic (~80%) and normal oleic (~50%) peanuts to produce segregating populations.ResultsA total of 539 F2 progenies were randomly selected to empirically determine each ahFAD2 genotype and the resulting fatty acid composition. Five of the six crosses segregated for the high oleic trait in a digenic fashion. The remaining cross was consistent with monogenic segregation because both parental genotypes were fixed for the ahFAD2A mutation. Segregation distortion was significant in ahFAD2A in one cross; however, the remaining crosses showed no distortion. Quantitative analyses revealed that dominance was incomplete for the wild type allele of ahFAD2, and both loci showed significant additive effects. Oleic and linoleic acid displayed five unique phenotypes, based on the number of ahFAD2 mutant alleles. Further, the ahFAD2 loci did exhibit pleiotropic interactions with palmitic (C16:0), oleic (C18:1), linoleic (C18:2) acids and the O/L ratio. Fatty acid levels in these progeny were affected by the parental genotype suggesting that other genes also influence fatty acid composition in peanut. As far as the authors are aware, this is the first study in which all of the nine possible ahFAD2 genotypes were quantitatively measured.ConclusionsThe inheritance of the high oleic trait initially was suggested to be controlled by dominant gene action from two homoeologous genes (ahFAD2A and ahFAD2B) exhibiting complete recessivity. Analyzing the ahFAD2 genotypes and fatty acid compositions of these segregating peanut populations clearly demonstrated that the fatty acid contents are quantitative in nature although much of the variability in the predominant fatty acids (oleic, linoleic, and palmitic) is controlled by only two loci.

Project description:BACKGROUND:Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to conduct genetic analyses and molecular breeding. Cultivated peanut (A. hypogaea L.), an important oil crop worldwide, is an allotetraploid (AABB, 2n = 4× = 40) plant species. Because of its complex genome, genomic marker development has been very challenging. However, sequencing of cultivated peanut genome allowed us to develop genomic markers and construct a high-density physical map. RESULTS:A total of 8,329,496 SSRs were identified, including 3,772,653, 4,414,961, and 141,882 SSRs that were distributed in subgenome A, B, and nine scaffolds, respectively. Based on the flanking sequences of the identified SSRs, a total of 973,984 newly developed SSR markers were developed in subgenome A (462,267), B (489,394), and nine scaffolds (22,323), with an average density of 392.45 markers per Mb. In silico PCR evaluation showed that an average of 88.32% of the SSR markers generated only one in silico-specific product in two tetraploid A. hypogaea varieties, Tifrunner and Shitouqi. A total of 39,599 common SSR markers were identified among the two A. hypogaea varieties and two progenitors, A. duranensis and A. ipaensis. Additionally, an amplification effectiveness of 44.15% was observed by real PCR validation. Moreover, a total of 1276 public SSR loci were integrated with the newly developed SSR markers. Finally, a previously known leaf spot quantitative trait locus (QTL), qLLS_T13_A05_7, was determined to be in a 1.448-Mb region on chromosome A05. In this region, a total of 819 newly developed SSR markers were located and 108 candidate genes were detected. CONCLUSIONS:The availability of these newly developed and public SSR markers both provide a large number of molecular markers that could potentially be used to enhance the process of trait genetic analyses and improve molecular breeding strategies for cultivated peanut.

Dataset Information

Stable QTLs for Plant Height on Chromosome A09 Identified From Two Mapping Populations in Peanut (Arachis hypogaea L.).

Publications

Stable QTLs for Plant Height on Chromosome A09 Identified From Two Mapping Populations in Peanut (<i>Arachis hypogaea</i> L.).

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