Genome-wide association analysis detecting significant single nucleotide polymorphisms for chlorophyll and chlorophyll fluorescence parameters in soybean (Glycine max) landraces

Hao, Dejun; Chao, Maoni; Yin, Zhitong; Yu, Deyue

doi:10.1007/s10681-012-0697-x

Cited by 74 publications

(54 citation statements)

References 67 publications

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“…In MLM, PCs from PCA and kinship (K) matrix analyses were used as the covariate (Bradbury et al, 2007;Hao et al, 2012). In MLM, PCs from PCA and kinship (K) matrix analyses were used as the covariate (Bradbury et al, 2007;Hao et al, 2012).…”

Section: Phenotypic Data Analysesmentioning

confidence: 99%

Genome‐Wide Association Study of Resistance to Cassava Green Mite Pest and Related Traits in Cassava

et al. 2018

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Cassava green mite [CGM, Mononychellus tanajoa (Bondar)] is a dry‐season pest that usually feeds on the underside of young leaves causing leaf chlorosis, stunted growth, and root yield reduction by 80%. Since cassava (Manihot esculenta Crantz) leaves and roots serve as a primary staple food source, a decline in cassava yield can lead to household food, nutrition, and income insecurity. To evaluate the existence of CGM resistance alleles in the available germplasm, a diversity panel of 845 advanced breeding lines obtained from IITA, CIAT, and the National Root Crops Research Institute (NRCRI) were evaluated for CGM severity (CGMS), leaf pubescence (LP), leaf retention (LR), stay green, shoot tip compactness, and shoot tip size. A genome‐wide association mapping detected 35 single‐nucleotide polymorphisms (SNPs) markers significantly associated with CGMS, LP, and LR on chromosome 8. Colocalization of the most significant SNP associated with CGMS, LP, and LR on chromosome 8 is possibly an indication of pleiotropy or the presence of closely linked genes that regulate these traits. Seventeen candidate genes were found to be associated to CGM resistance. These candidate genes were subdivided into seven categories according to their protein structure namely, Zn finger, pentatricopeptide, MYB, MADS, homeodomain, trichome birefringence‐related protein, and ethylene‐responsive transcription factor genes. This study revealed significant loci associated with CGM, not previously reported, which together represent potential sources for the ongoing effort to develop multiple pest‐ and disease‐resistant cassava cultivars.

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Section: Phenotypic Data Analysesmentioning

confidence: 99%

Genome‐Wide Association Study of Resistance to Cassava Green Mite Pest and Related Traits in Cassava

et al. 2018

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“…The information obtained could possibly be used to improve the PSMT model and to gain new insight in the functioning of the components of the photosynthetic machinery (Belyaeva et al, 2016). Of course there is also ample room for progress by studying jointly parameters derived from ChlF measurements and molecular and biochemical markers (Hao et al, 2012; Mladenov et al, 2015; Yin et al, 2015). …”

Section: Limitations Originating From the Theoretical Background Recmentioning

confidence: 99%

A User’s View of the Parameters Derived from the Induction Curves of Maximal Chlorophyll a Fluorescence: Perspectives for Analyzing Stress

et al. 2016

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Analysis of the fast kinetics of the induction curve of maximal fluorescence represents a relatively recent development for chlorophyll a fluorescence measurements. The parameters of the so-called JIP-test are exploited by an increasingly large community of users to assess plant stress and its consequences. We provide here evidence that these parameters are capable to distinguish between stresses of different natures or intensities, and between stressed plants of different genetic background or at different developmental stages at the time of stress. It is, however, important to keep in mind that the JIP-test is inherently limited in scope, that it is based on assumptions which are not fully validated and that precautions must be taken to ensure that measurements are meaningful. Recent advances suggest that some improvements could be implemented to increase the reliability of measurements and the pertinence of the parameters calculated. We moreover advocate for using the JIP-test in combination with other techniques to build comprehensive pictures of plant responses to stress.

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“…To minimize the effects of environmental factors, the best linear unbiased predictions (BLUPs) for DSI in each maize inbred line over years were also evaluated using PROC MIXED for further association analysis (Kump et al 2011;Hao et al 2012a). …”

Section: Phenotypic Data Analysismentioning

confidence: 99%

Identification of significant single nucleotide polymorphisms for resistance to maize rough dwarf disease in elite maize (Zea mays L.) inbred lines

Hao¹,

Cheng²,

Chen³

et al. 2014

Euphytica

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Maize rough dwarf disease (MRDD) is a devastating viral disease that causes considerable yield losses in maize worldwide. Identifying quantitative trait loci underlying resistance to MRDD is important for genetic improvement of maize. In this study, 184 elite maize inbred lines from modern breeding programs were evaluated in three years to identify QTLs for MRDD resistance using 3072 single-nucleotide polymorphisms (SNPs) via genome-wide association analysis. The analysis revealed abundant phenotypic diversity in the studied population. All tested maize inbred lines were divided into two subpopulations based on a Bayesian model, and the linkage disequilibrium (LD) level differed among chromosomes, with an intra-chromosomal average of 1,000-1,500 kb. After correction for multiple testing, 21 SNPs were identified for MRDD resistance in different years as well as for BLUPs (the best linear unbiased predictions) of MRDD resistance based on the MLM model, one SNP of PZE-101245575 was stably possessed the most promising association. Several SNPs were located in or close to previously reported quantitative trait loci for MRDD resistance. The significant SNPs identified in this study will be helpful for further understanding the genetic basis of MRDD resistance, and might facilitate the pyramiding of favorable alleles for high resistance to MRDD in future marker-assisted selection schemes in maize.

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Genome-wide association analysis detecting significant single nucleotide polymorphisms for chlorophyll and chlorophyll fluorescence parameters in soybean (Glycine max) landraces

Cited by 74 publications

References 67 publications

Genome‐Wide Association Study of Resistance to Cassava Green Mite Pest and Related Traits in Cassava

Genome‐Wide Association Study of Resistance to Cassava Green Mite Pest and Related Traits in Cassava

A User’s View of the Parameters Derived from the Induction Curves of Maximal Chlorophyll a Fluorescence: Perspectives for Analyzing Stress

Identification of significant single nucleotide polymorphisms for resistance to maize rough dwarf disease in elite maize (Zea mays L.) inbred lines

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