HAL Id: hal-02820815
https://hal.inrae.fr/hal-02820815
Submitted on 6 Jun 2020
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Identification of orthologous regions associated with
tissue growth under water-limited conditions
Genevieve M Aquino, C. Bencivenni, B. Boussuge, Jill E Cairns, Brigitte
Courtois, G. F. Davenport, S. Impa, D. C. Liu, Ramil Mauleon, J. M. Ribaut,
et al.
To cite this version:
Genevieve M Aquino, C. Bencivenni, B. Boussuge, Jill E Cairns, Brigitte Courtois, et al.. Identification
of orthologous regions associated with tissue growth under water-limited conditions. Generation
Chal-lenge Program Annual Research Meeting 2008, Sep 2008, Bangkok, Thailand. 2008. �hal-02820815�
Identification of orthologous regions associated
with tissue growth under water-limited conditions
Rice and maize under experimental conditions
Identification of QTLs associated with leaf growth
The Vandana/Moroberekan backcross population was evaluated in the field over three seasons (2005-2007). Leaf expansion and morphogenesis were measured and QTL identified.
i) rice
GM Aquino1, C Bencivenni2, B Boussuge2, JE Cairns1, B Courtois3, GF
Davenport2, S Impa1, DC Liu1, R Mauleon1, JM Ribaut2, R Serraj1, T
Shah2, R Torres1, C Welcker4 and F Tardieu4
1International Rice Research Institute (IRRI), 2International Centre for Maize and
Wheat Improvement (CIMMYT), 3CIRAD, 4INRA-AGRO, Laboratoire d’Ecophysiologie
des Plantes sous Stress Environmentaux
Leaf elongation rate of the 6th leaf was measured in the greenhouse on 200
RILs from a mapping population developed at CIMMYT in the sixth inbreeding level from the cross between 2 tropical maize inbred lines, Ac7645 and Ac7729/TZSRW (Welcker et al. 2006).
ii) maize
This work is part of the Generation Challenge Program Special Funded Project 15 “Determination of a common genetic basis for tissue growth rate under water-
limited conditions across plant organs and genomes.” Plant recovery from early season drought is related to the
amount of biomass retained during stress and biomass production after the end of stress. Reduction in leaf expansion is one of the first responses to water deficit. It is assumed that the control of tissue development under water deficit contributes to traits such as early vigor, as well as maintenance of growth of reproductive organs. To dissect the underlying mechanisms controlling tissue expansion under water-limited conditions, we used a multilevel approach combining quantitative genetics and genomics.
To identify orthologous genetic regions controlling tissue growth under water-limited conditions a series of QTL mapping and microarray gene expression studies were conducted in rice and maize. Results of differentially expressed genes from microarray experiments, QTLs and candidate genes related to growth in the different species are compared on consensus maps (within species) and then on synteny maps (between species), to identify common genetic regions between rice and maize.
QTLs associated with leaf growth in rice and maize
Conclusions and future perspectives
Chr 1 Chr 2 Chr 5 Chr 8
Lw a b c
1 2 1 2 31 21 23456 1 2 1 2 3Lw a1 2b1 23456c 1 2 1 2 3Lw a1 2b1 23456 1 2 1 2 3c Lw a1 2b1 23456c
QTLs identified for leaf growth and leaf growth response to water deficit. Each strip represents a combination of chromosome, experiment and trait. Blue = non-signficant QTL, yellow = LOD>2.4, red = LOD>3.0. QTLs detected for final leaf length (Lw) in 2004 (1) and 2005 (2), slope of the response to evaporative demand (a) in 2005 (1) and the x-intercept of the same relationship (2), and slope of the responses of leaf elongation rate to predawn leaf water potential in 2004 (1), 2005 (2), over the whole dataset (3) and the x-intercept of the same relationship in 2004 (5) and 2006 (6).
Taken from Welcker et al. 2006
Identification of orthologous regions in maize and rice
QTL positions in the physical genome were inferred using coordinates of the corresponding markers onto the physical genome. Coordinates of rice SSR markers on the physical map were determined by searching the Gramene annotation of the TIGR rice genome ver5 (www.gramene.org/) for positions of well-durated markers or a similarity search using the BLAST-like Alignment Tool (BLAT, Kent 2002) against the full-length contigs of TIGR rice genome ver 5.0 (tile size = 6-8) with the published sequence or primers of SSR markers on Gramene. Coordinates of maize RFLP markers on the physical maps were determined by searching the Maize Genome Sequence (www.maizesequence.org) annotation of the draft sequence available for available annotation of the positions of the maize markers. Rice-maize genome synteny information was obtained from Gramene.
Comparison of rice QTL and gene expression data
Microarray was performed on the 6th leaf of Vandana, Moroberekan and 2
backcross lines under well-watered and water-limited (FTSW 0.5) conditions. Differentially expressed gene (DEG) aggregates were computed from comparisons between the two water levels. QTL and DEG aggregates were plotted on the rice genome using TIGR (Osa1 release 5).
Many QTL were identified in rice and maize controlling leaf growth under water-limited and well-watered conditions. In each crop, several regions were detected across traits and/or experiments.
Orthologous regions controlling tissue growth under water-limited conditions in rice and maize
Maize chromosome 2 to rice Maize chromosome 5 to rice
The identification of syntenic regions between maize and rice is currently underway. In maize QTL identified on chromosomes 2 and 5 were also identified as QTL controlling leaf growth across experiments and containing DEG aggregates.
Differentially expressed gene aggregates in rice: colocalization with QTL associated with leaf growth
Several QTL region s
associated with leaf growth under drought stress contained differentially
expressed gene (DEG )
aggregates, although this was not consistent across all genotypes.
Chromosome 2 between markers RM318 and RM168
Chromosome 4 between markers RM241 and RM348
Differentially expressed gene aggregates identified in two regions on chromosomes 2 and 4 associated with leaf growth under drought stress
To identify a common genetic basis for tissue growth under water-limited conditions the mechanisms controlling leaf growth under water-deficit in rice and maize were dissected using QTL mapping and transcript profiling. Ongoing analysis of orthologous regions has identified several syntenic regions between rice and maize.
Number of leaves Leaf elongation rate Leaf elongation rate
Number of leaves (496 Cd) Number of leaves (695 Cd) Leaf dry weight (496 Cd) Leaf dry weight (695 Cd) Partitioning to leaves (695 Cd) Increase (slope) in leaf area
Decrease in leaf dry weight Increase (slope) in leaf area (control) Increase (slope) in leaf dry weight (control) Leaf area (stress)
Leaf dry weight (control) Leaf dry weight (stress) Leaf elongation rate (stress) Partitioning to leaves (stress) Partitioning to leaves (control)
1 2 3 4 5 6 7 8 9 10 11 12
2005
2006
2007
QTLs identified for leaf growth and leaf growth response to water deficit under fiel d conditions in 2005 (rainfed), 2006 (drought stress) and 2007 (drought stress and well- watered). For boxes on the right hand side of chromosomes, the Vandana allele increased the trait
Maize Rice
