Fine mapping of qhir1 influencing in vivo haploid induction in maize

Dong, Xiaomei; Xu, Xiaowei; Miao, Jianjun; Li, L.; Zhang, Di; Mi, Xuefei; Liu, C.; Tian, Xiaolong; Melchinger, Albrecht E.; Chen, S.

doi:10.1007/s00122-013-2086-9

Cited by 74 publications

(74 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The segment identified on chromosome 1 spanned 3.97 Mb on the physical map, overlapped with all support intervals of qhir1 from four QTL mapping populations ( Figure 3, A-C; Prigge et al 2012), and was denoted qhir12. Adjacent to this region was a shorter 0.54-Mb segment denoted qhir11 ( Figure 2B), which harbored the 243-kb region fine mapped by Dong et al (2013) and was fixed in all inducers and significant in the Clopper-Pearson test (Table 1); for these reasons, this segment was also considered in our subsequent analyses.The qhir12 segment was not detected by Dong et al (2013), as it lies 985 kb outside (downstream) the marker interval originally chosen for fine mapping, but their results from cross 1680 3 UH400 provide strong evidence in support of a second region linked to their 243-kb fine-mapped segment, because the effect of the entire qhir1 region found in the F 2 generation (see figure 2 in Dong et al 2013) was more than twice the effect of the 243-kb segment segregating in F 3 progeny of recombinant F 2 individuals (see figure 3 in Dong et al 2013). Thus, the 243-kb segment making up about half of the qhir11 segment detected in our study, explained less than one quarter of the genetic variance of HI attributable to QTL qhir1.…”

mentioning

confidence: 99%

“…Based on breeders' knowledge or pedigree information, these lines were assigned to seven germplasm groups: European Dent The 10 genomic segments with the highest CHE scores were obtained from a genome-wide scan of 53 inducers with the CHE test. One additional segment (qhir11) harbors the 243 kb segment fine-mapped by Dong et al (2013). NI, noninducers; **P , 0.001, *P , 0.01; NS, not significant.…”

mentioning

confidence: 99%

“…Various threshold t values can be chosen depending on the population under study. In our study, the objective was to detect the genomic segments required for HI among all maize inducers; therefore, we chose the very stringent threshold t = 1.0, which results in detection of long genomic segments fixed among all 53 inducers.In the second step, a formal statistical test was carried out for the top n (n = 10 in our study) segments with the highest CHE scores detected in the first step (details were described in File S3) as well as for the qhir11 segment that was not among the 10 segments with the highest CHE score but for which prior knowledge existed from Dong et al (2013). Briefly, we calculated for each genomic segment separately a Clopper-Pearson confidence interval for testing the hypothesis that transmission of the detected segment through known pedigrees of the cases cannot be explained by chance alone in the development of new inducers.…”

mentioning

confidence: 99%

“…The most comprehensive study with four biparental populations (Prigge et al 2012) mapped this QTL, termed qhir1, to bin 1.04 and hypothesized that it is required for HI, but QTL positions and 1-LOD support intervals differed substantially among populations. In another study with population 1680 3 UH400, Dong et al (2013) fine mapped a 3.57-Mb region between markers umc1917 and bnlg1811, which targeted the QTL qhir1 and identified a 243-kb region with significant effect on HI. Both studies employed inbred UH400 as inducer parent, which limits the inference on HI to this specific inducer line.…”

mentioning

confidence: 99%

“…Moreover, in view of the uncertainties associated with the exact QTL position, concentrating the fine mapping on a very narrow region carries the risk of overlooking important adjacent segments. Therefore, our objectives were to (i) detect selective sweeps for HI in a worldwide collection of inducers (cases) and noninducers (controls) by a genomewide association study (GWAS); (ii) identify a candidate region(s) underlying qhir1; (iii) validate the fine-mapping results reported by Dong et al (2013) in a broader set of genetic material with an independent, complementary approach; and (iv) resequence the qhir1 region for identification of candidate genes involved in HI in maize. For application of GWAS, we developed a novel method that can deal with almost perfect confounding between genetic ancestry and trait expression.…”

mentioning

confidence: 99%

See 4 more Smart Citations

The Genetic Basis of Haploid Induction in Maize Identified with a Novel Genome-Wide Association Method

Schrag

Peis

et al. 2016

Genetics

View full text Add to dashboard Cite

In vivo haploid induction (HI) triggered by pollination with special intraspecific genotypes, called inducers, is unique to Zea mays L. within the plant kingdom and has revolutionized maize breeding during the last decade. However, the molecular mechanisms underlying HI in maize are still unclear. To investigate the genetic basis of HI, we developed a new approach for genome-wide association studies (GWAS), termed conditional haplotype extension (CHE) test that allows detection of selective sweeps even under almost perfect confounding of population structure and trait expression. Here, we applied this test to identify genomic regions required for HI expression and dissected the combined support interval (50.34 Mb) of the QTL qhir1, detected in a previous study, into two closely linked genomic segments relevant for HI expression. The first, termed qhir11 (0.54 Mb), comprises an already fine-mapped region but was not diagnostic for differentiating inducers and noninducers. The second segment, termed qhir12 (3.97 Mb), had a haplotype allele common to all 53 inducer lines but not found in any of the 1482 noninducers. By comparing resequencing data of one inducer with 14 noninducers, we detected in the qhir12 region three candidate genes involved in DNA or amino acid binding, however, none for qhir11. We propose that the CHE test can be utilized in introgression breeding and different fields of genetics to detect selective sweeps in heterogeneous genetic backgrounds.KEYWORDS in vivo haploid induction; selective sweep; genome-wide association study; population structure; Zea mays L T HE double haploid (DH) technology based on in vivo haploid induction (HI) has become one of the most important tools in maize breeding during the past decade and is replacing the conventional method of line development by recurrent selfing . The success of this new technology became possible, because dozens of maize inducer lines have been developed worldwide (reviewed in Supplemental Material, File S1) which, when used as pollinators, trigger the production of seeds with haploid embryo at an acceptable rate, i.e., .2% . Double fertilization followed by elimination of the inducer chromosomes in the embryo at later developmental stages (Li et al. 2009;Xu et al. 2013) as well as parthenogenesis (Sarkar and Coe 1966;Beckert et al. 2008) HI in maize, but a proof of these hypotheses requires profound knowledge about the genetic and physiological factors underlying this phenomenon. All previous QTL mapping studies for unraveling the genetic architecture of HI detected a major QTL on chromosome 1 (Röber 1999;Beckert et al. 2008; Prigge et al. 2012). The most comprehensive study with four biparental populations (Prigge et al. 2012) mapped this QTL, termed qhir1, to bin 1.04 and hypothesized that it is required for HI, but QTL positions and 1-LOD support intervals differed substantially among populations. In another study with population 1680 3 UH400, Dong et al. (2013) fine mapped a 3.57-Mb region between markers umc1917 and bnlg1811, w...

show abstract

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations