Fine Mapping and Haplotype Structure Analysis of a Major Flowering Time Quantitative Trait Locus on Maize Chromosome 10

Ducrocq, Sébastien; Giauffret, Catherine; Madur, Delphine; Combes, Valérie; Dumas, Fabrice; Jouanne, Sophie; Coubriche, Denis; Jamin, Philippe; Moreau, Laurence; Charcosset, Alain

doi:10.1534/genetics.109.106922

Cited by 60 publications

(59 citation statements)

References 42 publications

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“…The QTL explaining the most variation and expressing the strongest allele effects mapped to chromosome 10 ( Figs. 1 and 2); the importance of this region has been observed consistently across maize photoperiod mapping studies (12,18,19). Alleles at this locus have highly heterogeneous effects, even within the tropical subgroup of founder lines ( Fig.…”

Section: Resultssupporting

confidence: 54%

“…The highest resolution was obtained in the Ki11 population, where the QTL was narrowed to a 443-kbp region containing six predicted genes in the reference sequence, including ZmCCT, a homologue of rice Ghd7 (SI Appendix, Fig. S6) (19). Fine-mapping of the maize-teosinte chromosome 10 QTL was conducted by using a BC 2 S 3 family segregating for a 51-Mbp region around the QTL.…”

Section: Resultsmentioning

confidence: 99%

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ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize

Hung

Shannon

Tian

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

306

354

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Teosinte, the progenitor of maize, is restricted to tropical environments in Mexico and Central America. The pre-Columbian spread of maize from its center of origin in tropical Southern Mexico to the higher latitudes of the Americas required postdomestication selection for adaptation to longer day lengths. Flowering time of teosinte and tropical maize is delayed under long day lengths, whereas temperate maize evolved a reduced sensitivity to photoperiod. We measured flowering time of the maize nested association and diverse association mapping panels in the field under both short and long day lengths, and of a maize-teosinte mapping population under long day lengths. Flowering time in maize is a complex trait affected by many genes and the environment. Photoperiod response is one component of flowering time involving a subset of flowering time genes whose effects are strongly influenced by day length. Genome-wide association and targeted high-resolution linkage mapping identified ZmCCT, a homologue of the rice photoperiod response regulator Ghd7, as the most important gene affecting photoperiod response in maize. Under long day lengths ZmCCT alleles from diverse teosintes are consistently expressed at higher levels and confer later flowering than temperate maize alleles. Many maize inbred lines, including some adapted to tropical regions, carry ZmCCT alleles with no sensitivity to day length. Indigenous farmers of the Americas were remarkably successful at selecting on genetic variation at key genes affecting the photoperiod response to create maize varieties adapted to vastly diverse environments despite the hindrance of the geographic axis of the Americas and the complex genetic control of flowering time.genetic diversity | quantitative trait locus T he rapid spread of agriculture from the Fertile Crescent was enabled in part by the East-West axis of Eurasia, permitting crop cultivation to spread across large geographic regions at a common latitude (1). The relatively simple genetic control of flowering time of the key crops domesticated in the Fertile Crescent, wheat and barley (2), coupled with a predominantly selffertilizing mating system, also facilitated colonization of new environments by rare mutants with large effects on flowering time responses to day length and temperature.In contrast, the spread of maize from its origin in Southern Mexico 6 to 10,000 y ago was relatively slow (1), hindered by the North-South axis of the Americas. Maize (Zea mays L. subsp. mays) was domesticated from the Mexican native teosinte Zea mays L. subsp. parviglumis (3), a species adapted to day lengths less than 13 h. Under the longer day lengths of higher latitudes, teosinte flowers very late or not at all (4). From its Meso-American origin, maize was spread by early humans to geographically and ecologically diverse environments from Canada to Chile well before the arrival of Columbus to the Americas (5, 6), requiring its adaptation to long day lengths. Thus, although the spread of maize occurred later than that of wheat, ...

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Section: Resultssupporting

confidence: 54%

Section: Resultsmentioning

confidence: 99%

ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize

Hung

Shannon

Tian

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

306

354

View full text Add to dashboard Cite

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“…It displayed marked variation in flowering time, from extremely early materials to photoperiod sensitive tropical materials. These features have contributed to the discovery of interesting associations based on candidate gene approaches such as Vgt1 (Ducrocq et al, 2008), ZmCCT (Ducrocq et al, 2009) and Opaque2 (Manicacci et al, 2009), with a first genome-wide scan in this panel revealing ZCN8 as a major gene corresponding to Vgt2, 8Mb from Vgt1, as well as other QTLs involved in flowering time (Bouchet et al, 2013). Our study highlighted the high variation in this panel regarding plant architecture and grain yield related traits, and contrasted genetic architectures for these traits.…”

Section: Discussionmentioning

confidence: 62%

“…Association studies on diversity panels are effective for identifying genetic variants associated with phenological and morphological traits in maize (Thornsberry et al, 2001;Flint-Garcia et al, 2005;CamusKulandaivelu et al, 2006;Ducrocq et al, 2008Ducrocq et al, , 2009Durand et al, 2012;Romay et al, 2013;Bouchet et al, 2013). In the current study, 375 lines of maize originating from the tropics, USA and Europe were successfully phenotyped for 24 ecologically and agronomically important traits related to (i) phenology, (ii) plant architecture, (iii) ear and yield components and (iv) tassel architecture.…”

Section: Introductionmentioning

confidence: 99%

Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits

et al. 2016

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Plant architecture, phenology and yield components of cultivated plants have repeatedly been shaped by selection to meet human needs and adaptation to different environments. Here we assessed the genetic architecture of 24 correlated maize traits that interact during plant cycle. Overall, 336 lines were phenotyped in a network of 9 trials and genotyped with 50K singlenucleotide polymorphisms. Phenology was the main factor of differentiation between genetic groups. Then yield components distinguished dents from lower yielding genetic groups. However, most of trait variation occurred within group and we observed similar overall and within group correlations, suggesting a major effect of pleiotropy and/or linkage. We found 34 quantitative trait loci (QTLs) for individual traits and six for trait combinations corresponding to PCA coordinates. Among them, only five were pleiotropic. We found a cluster of QTLs in a 5 Mb region around Tb1 associated with tiller number, ear row number and the first PCA axis, the latter being positively correlated to flowering time and negatively correlated to yield. Kn1 and ZmNIP1 were candidate genes for tillering, ZCN8 for leaf number and Rubisco Activase 1 for kernel weight. Experimental repeatabilities, numbers of QTLs and proportion of explained variation were higher for traits related to plant development such as tillering, leaf number and flowering time, than for traits affected by growth such as yield components. This suggests a simpler genetic determinism with larger individual QTL effects for the first category. Although technology to support this process has dramatically evolved, especially in recent decades, breeders' objectives have not fundamentally changed over the last 10 000 years. They still have to overcome the difficulty of conducting multiple trait selection in different and variable environments and their choices are often trade-offs between an ideal plant architecture, product quality, yield and adaptation to targeted environments. Low cost genotyping can accelerate the selection of large effect beneficial alleles and high throughput genotyping can improve the accuracy of breeding value predictions for multi-traits controlled by small effect quantitative trait loci (QTLs).In cereals, yield remains the main objective even though it may be negatively correlated with some quality traits. Yield is a complex trait to predict as it is the result of many trait interactions during plant development and growth. The objective is to combine plant architecture that maximizes light interception, phenology that synchronizes reproduction stage with optimal environmental conditions to minimize abortion, inflorescence architecture for optimal seed set, and numerous factors contributing to environmental adaptation and grain filling.

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“…Tropical maize exhibits delayed flowering time, increased plant height, and a greater total leaf number when grown in temperate latitudes with daily dark periods ,11 hr (Allison and Daynard 1979; Warrington and Kanemasu 1983a,b). Identifying the genes underlying maize photoperiod sensitivity will provide insight into the postdomestication evolution of maize and may reduce barriers to the use of diverse tropical germplasm resources for improving temperate maize production (Holland and Goodman 1995;Liu et al 2003;Ducrocq et al 2009).…”

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confidence: 99%

Genetic Control of Photoperiod Sensitivity in Maize Revealed by Joint Multiple Population Analysis

et al. 2010

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Variation in maize for response to photoperiod is related to geographical adaptation in the species. Maize possesses homologs of many genes identified as regulators of flowering time in other species, but their relation to the natural variation for photoperiod response in maize is unknown. Candidate gene sequences were mapped in four populations created by crossing two temperate inbred lines to two photoperiod-sensitive tropical inbreds. Whole-genome scans were conducted by high-density genotyping of the populations, which were phenotyped over 3 years in both short-and long-day environments. Joint multiple population analysis identified genomic regions controlling photoperiod responses in flowering time, plant height, and total leaf number. Four key genome regions controlling photoperiod response across populations were identified, referred to as ZmPR1-4. Functional allelic differences within these regions among phenotypically similar founders suggest distinct evolutionary trajectories for photoperiod adaptation in maize. These regions encompass candidate genes CCA/LHY, CONZ1, CRY2, ELF4, GHD7, VGT1, HY1/SE5, TOC1/PRR7/PPD-1, PIF3, ZCN8, and ZCN19.

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Fine Mapping and Haplotype Structure Analysis of a Major Flowering Time Quantitative Trait Locus on Maize Chromosome 10

Cited by 60 publications

References 42 publications

ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize

ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize

Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits

Genetic Control of Photoperiod Sensitivity in Maize Revealed by Joint Multiple Population Analysis

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