IC4R006-Phenomics-2015-26104576 - Revision history

Liman: /* Research Findings */

2016-07-28T17:23:29Z

‎Research Findings

Liman: /* Research Findings */

2016-07-28T17:19:45Z

‎Research Findings

Liman: /* Research Findings */

2016-07-28T17:02:51Z

‎Research Findings

Liman: /* Research Findings */

2016-07-28T17:01:14Z

‎Research Findings

Liman: /* Research Findings */

2016-07-28T16:59:52Z

‎Research Findings

Liman: /* The Background of This Project */

2016-07-28T16:58:26Z

‎The Background of This Project

Liman: /* Plant Materials & Treatment */

2016-07-28T15:31:58Z

‎Plant Materials & Treatment

Liman: /* Corresponding Author */

2016-07-28T15:30:19Z

‎Corresponding Author

Liman: Created page with "==Project Title== * '''Field phenomics for response of a rice diversity panel to tenenvironments in Senegal and Madagascar. 1. Plant phenological traits''' ==The Background o..."

2016-07-28T15:29:18Z

Created page with "==Project Title== * '''Field phenomics for response of a rice diversity panel to tenenvironments in Senegal and Madagascar. 1. Plant phenological traits''' ==The Background o..."

New page

==Project Title==
* '''Field phenomics for response of a rice diversity panel to tenenvironments in Senegal and Madagascar. 1. Plant phenological traits'''

==The Background of This Project==
*

==Plant Materials & Treatment==
*

==Research Findings==

==Labs working on this Project==
* Cirad, Umr AGAP (Dept. BIOS) and Upr AIDA (Dept. ES), F-34398, Montpellier, France
* IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines
* Africa Rice Center, Sahel Station, P.B. 96, St. Louis, Senegal
* Université d’Antananarivo, Département de Biologie et Ecologie Végétales, BP 906, Antananarivo 101, Madagascar
* SRR FOFIFA, BP 230, Antsirabe 110, Madagascara

==Corresponding Author==

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 * The environmentsThe six sowing dates in Senegal subjected the crop to very differ-ent weather and day length conditions (Fig. 1). Weather variablesare presented in Fig. 1A as averages for the initial 80 d of the cropas a rough measure of conditions during pre-floral developmentstages. The first three sowing dates were associated with low min-imum air humidity (RHmin) averaging less than 30%, while meanminimum meanminimum temperature increased from 16.4 (February crop) to 19.0(April crop)℃. Mean and maximal temperatures increased at a sim-ilar rate, with a constant mean diurnal temperature amplitude ofabout 15℃. Astronomic day length varied between 11.05 h in winter and12.97 h in summer (wet season) (Fig. 1B). The July crop had thelongest days at sowing but experienced decreasing day lengththroughout its life cycle. Conversely, the February crop had theshortest days at sowing but experienced increasing day lengththroughout its cycle.
-[[File:IC4R006-Phenomics-2015-26104576-f1.png |center |thumb |800px |'''Fig. 1. Graph A: Weather variables averaged for the period from sowing to 80 d after sowing at the Senegal site. Tmax, Tmean, Tminare maximum, mean and minimum airtemperature at 2 m, respectively. RH is minimum daily relative air humidity. PET is potential evaporation according to FAO standard. The recommended sowing dates for thehot–dry season (HDS) and the wet season (WS) are indicated. Graph B: Astronomic day length at sowing''']]
+[[File:IC4R006-Phenomics-2015-26104576-f1.png |center |thumb |400px |'''Fig. 1. Graph A: Weather variables averaged for the period from sowing to 80 d after sowing at the Senegal site. Tmax, Tmean, Tminare maximum, mean and minimum airtemperature at 2 m, respectively. RH is minimum daily relative air humidity. PET is potential evaporation according to FAO standard. The recommended sowing dates for thehot–dry season (HDS) and the wet season (WS) are indicated. Graph B: Astronomic day length at sowing''']]
 * floweringSenegal. Only four check varieties were replicated for each ofthe 6 sowing dates in the augmented design of the experimentin Senegal. No block (replication) effects were observed accordingto ANOVA, whereas genotype, sowing date and date X genotypeeffects were highly significant (P < 0.0001) (Table 2A). Broad-senseheritability on the basis of family means was high at h2= 0.95(Table 2C).Madagascar. All 209 accessions were replicated in both yearsand locations. There was a significant block (replication) effecton time to flowering (P < 0.0001, F = 6.0) but it was negligiblein size as compared to the year (F = 156), location (F = 30783)and genotype (F = 367) effects, which were also highly significant(P < 0.0001) (Table 2B). Broad-sense heritability of time to floweringwas h2= 0.98 (Table 2C).
-[[File:IC4R006-Phenomics-2015-26104576-f2.png |center |thumb |800px |'''Fig. 2. Duration from sowing to maximum flowering for four check genotypes. (A) Observations for 6 sowing dates in Senegal in 2009 (means and SEM for 6 replications).(B) Observations for Madagascar at mid altitude (857 m asl) and high altitude (1497 m asl) for 2009 and 2010 (means and SEM of 3 replications. The straight lines connectthe 2-year means for two altitudes. No data for cv. Chomrong were available for high altitude.''']]
+[[File:IC4R006-Phenomics-2015-26104576-f2.png |center |thumb |500px |'''Fig. 2. Duration from sowing to maximum flowering for four check genotypes. (A) Observations for 6 sowing dates in Senegal in 2009 (means and SEM for 6 replications).(B) Observations for Madagascar at mid altitude (857 m asl) and high altitude (1497 m asl) for 2009 and 2010 (means and SEM of 3 replications. The straight lines connectthe 2-year means for two altitudes. No data for cv. Chomrong were available for high altitude.''']]
 * SenegalThree contrasting patterns of F across sowing dates in Senegalwere observed (Fig. 3). The majority of genotypes showed the short-est F when sown in July and a marked increase at earlier and later sowing dates (Fig. 3A). Genotypes within that group, however, haddifferent baseline duration. The shortest F for all sowing dates wasobserved for the temperate-japonica type Nipponbare (repeatedin Fig. 3B and C as reference). Strongly photoperiod-sensitive andquite uniform behavior was observed for some genotypes (Fig. 3B).The greatest F was observed in February crops and the shortest inSeptember crops, with a 3- to 4-fold difference in F. Lastly, somegenotypes showed a maximum of F for March or April sowing(Fig. 3C), similar to sorghum patterns of F (Dingkuhn et al., 2008).In contrast to the 2nd group, this group had a large diversity in theseasonal amplitude of variation in F.
-[[File:IC4R006-Phenomics-2015-26104576-f3.png |center |thumb |800px |'''Fig. 3. Selected cases of genotypic response of flowering time to sowing date in Senegal representing three distinctly different patterns.''']]
+[[File:IC4R006-Phenomics-2015-26104576-f3.png |center |thumb |500px |'''Fig. 3. Selected cases of genotypic response of flowering time to sowing date in Senegal representing three distinctly different patterns.''']]
 * SenegalMonomodal distributions of F across the germplasm panel wereobserved for sowings in July, September and October (Fig. 4). Forsowings in February, March and April, however, patterns werebimodal, with a second, smaller maximum at extremely high F(180–220 d). Consequently, a distinct group of germplasm becamephenotypically separated from the others during those months.
-[[File:IC4R006-Phenomics-2015-26104576-f4.png |center |thumb |800px |'''Fig. 3. Frequency histograms of days to flowering for the entire panel (all geneticgroups) as observed for 6 sowing dates in Senegal. Bimodal distributions wereobserved for Feb, Mar and Apr sowings, separating photoperiod-sensitive frominsensitive accessions.''']]
+[[File:IC4R006-Phenomics-2015-26104576-f4.png |center |thumb |800px |'''Fig. 4. Frequency histograms of days to flowering for the entire panel (all geneticgroups) as observed for 6 sowing dates in Senegal. Bimodal distributions wereobserved for Feb, Mar and Apr sowings, separating photoperiod-sensitive frominsensitive accessions.''']]
 * A strong linear correlation was observed for F between themid and high altitudes in Madagascar (Fig. 5A). A linear but morescattered correlation was also observed between F in Madagas-car (mid-altitude) and Senegal (July sowing) (Fig. 5B). Comparingcorrelations between F in Madagascar (high-altitude) and dif-ferent sowing dates in Senegal showed greatest R2and slopefor July (Fig. 5C). Both R2and slope dropped dramatically whensowing occurred after July (September, October). Consequently,correlations were nearly absent when F was compared betweencool environments in Senegal and Madagascar, but were strongbetween the cold environment in Madagascar and the most favor-able (warm–humid) environment in Senegal.
-[[File:IC4R006-Phenomics-2015-26104576-f5.png |center |thumb |800px |'''Fig. 5. Correlations among observed days to flowering for different environments for all genotypes pooled. (A) Madagascar high vs. mid altitude; (B) Madagascar mid altitudevs. Senegal July crop (wet season); (C) profile of correlations for Madagascar high altitude vs. 6 sowing dates in Senegal. For A and B the linear regression line and 95%confidence interval are indicated. The case of slope = 1 in 4C corresponds to the data in 4B.''']]
+[[File:IC4R006-Phenomics-2015-26104576-f5.png |center |thumb |500px |'''Fig. 5. Correlations among observed days to flowering for different environments for all genotypes pooled. (A) Madagascar high vs. mid altitude; (B) Madagascar mid altitudevs. Senegal July crop (wet season); (C) profile of correlations for Madagascar high altitude vs. 6 sowing dates in Senegal. For A and B the linear regression line and 95%confidence interval are indicated. The case of slope = 1 in 4C corresponds to the data in 4B.''']]
 * A significant negative correlation was observed between the dif-ference in F between high and mid altitude (altitude effect) and theabsolute F at mid altitude in Madagascar (Fig. 6A). Consequently,the altitude effect on F was greater in short- than long-durationmaterials. The altitude effect on F was also smaller in the majority ofphotoperiod-sensitive materials (Fig. 6B), assuming that photope-riod sensitivity was expressed by the index variable for photoperiodsensitivity, which was equal to F (March)/F (July) as observed inSenegal. Consequently, photoperiod-sensitive genotypes appearedto respond less to altitude than photoperiod-insensitive genotypes.It thus appears that there is a linkage between the genotypic alti-tude effect on F and other genotypic phenology parameters, suchas earliness and photoperiod sensitivity.
-[[File:IC4R006-Phenomics-2015-26104576-f6.png |center |thumb |800px |'''Fig. 6. Relationships between altitude effects on duration to flowering (difference high minus mid altitude) and other phenological traits for all genotypes pooled. (A) Altituderesponse vs. baseline duration at mid-altitude in Madagascar, with lines indicating linear regression line and 95% confidence interval; (B) index of photoperiod response inSenegal vs. altitude response in Madagascar.''']]
+[[File:IC4R006-Phenomics-2015-26104576-f6.png |center |thumb |500px |'''Fig. 6. Relationships between altitude effects on duration to flowering (difference high minus mid altitude) and other phenological traits for all genotypes pooled. (A) Altituderesponse vs. baseline duration at mid-altitude in Madagascar, with lines indicating linear regression line and 95% confidence interval; (B) index of photoperiod response inSenegal vs. altitude response in Madagascar.''']]
 ==Labs working on this Project==

← Older revision		Revision as of 17:19, 28 July 2016
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	[[File:IC4R006-Phenomics-2015-26104576-f2.png \|center \|thumb \|800px \|'''Fig. 2. Duration from sowing to maximum flowering for four check genotypes. (A) Observations for 6 sowing dates in Senegal in 2009 (means and SEM for 6 replications).(B) Observations for Madagascar at mid altitude (857 m asl) and high altitude (1497 m asl) for 2009 and 2010 (means and SEM of 3 replications. The straight lines connectthe 2-year means for two altitudes. No data for cv. Chomrong were available for high altitude.''']]		[[File:IC4R006-Phenomics-2015-26104576-f2.png \|center \|thumb \|800px \|'''Fig. 2. Duration from sowing to maximum flowering for four check genotypes. (A) Observations for 6 sowing dates in Senegal in 2009 (means and SEM for 6 replications).(B) Observations for Madagascar at mid altitude (857 m asl) and high altitude (1497 m asl) for 2009 and 2010 (means and SEM of 3 replications. The straight lines connectthe 2-year means for two altitudes. No data for cv. Chomrong were available for high altitude.''']]
		+
		+	* SenegalThree contrasting patterns of F across sowing dates in Senegalwere observed (Fig. 3). The majority of genotypes showed the short-est F when sown in July and a marked increase at earlier and later sowing dates (Fig. 3A). Genotypes within that group, however, haddifferent baseline duration. The shortest F for all sowing dates wasobserved for the temperate-japonica type Nipponbare (repeatedin Fig. 3B and C as reference). Strongly photoperiod-sensitive andquite uniform behavior was observed for some genotypes (Fig. 3B).The greatest F was observed in February crops and the shortest inSeptember crops, with a 3- to 4-fold difference in F. Lastly, somegenotypes showed a maximum of F for March or April sowing(Fig. 3C), similar to sorghum patterns of F (Dingkuhn et al., 2008).In contrast to the 2nd group, this group had a large diversity in theseasonal amplitude of variation in F.
		+
		+	[[File:IC4R006-Phenomics-2015-26104576-f3.png \|center \|thumb \|800px \|'''Fig. 3. Selected cases of genotypic response of flowering time to sowing date in Senegal representing three distinctly different patterns.''']]
		+
		+	* SenegalMonomodal distributions of F across the germplasm panel wereobserved for sowings in July, September and October (Fig. 4). Forsowings in February, March and April, however, patterns werebimodal, with a second, smaller maximum at extremely high F(180–220 d). Consequently, a distinct group of germplasm becamephenotypically separated from the others during those months.
		+
		+	[[File:IC4R006-Phenomics-2015-26104576-f4.png \|center \|thumb \|800px \|'''Fig. 3. Frequency histograms of days to flowering for the entire panel (all geneticgroups) as observed for 6 sowing dates in Senegal. Bimodal distributions wereobserved for Feb, Mar and Apr sowings, separating photoperiod-sensitive frominsensitive accessions.''']]
		+
		+	* A strong linear correlation was observed for F between themid and high altitudes in Madagascar (Fig. 5A). A linear but morescattered correlation was also observed between F in Madagas-car (mid-altitude) and Senegal (July sowing) (Fig. 5B). Comparingcorrelations between F in Madagascar (high-altitude) and dif-ferent sowing dates in Senegal showed greatest R2and slopefor July (Fig. 5C). Both R2and slope dropped dramatically whensowing occurred after July (September, October). Consequently,correlations were nearly absent when F was compared betweencool environments in Senegal and Madagascar, but were strongbetween the cold environment in Madagascar and the most favor-able (warm–humid) environment in Senegal.
		+
		+	[[File:IC4R006-Phenomics-2015-26104576-f5.png \|center \|thumb \|800px \|'''Fig. 5. Correlations among observed days to flowering for different environments for all genotypes pooled. (A) Madagascar high vs. mid altitude; (B) Madagascar mid altitudevs. Senegal July crop (wet season); (C) profile of correlations for Madagascar high altitude vs. 6 sowing dates in Senegal. For A and B the linear regression line and 95%confidence interval are indicated. The case of slope = 1 in 4C corresponds to the data in 4B.''']]
		+
		+	* A significant negative correlation was observed between the dif-ference in F between high and mid altitude (altitude effect) and theabsolute F at mid altitude in Madagascar (Fig. 6A). Consequently,the altitude effect on F was greater in short- than long-durationmaterials. The altitude effect on F was also smaller in the majority ofphotoperiod-sensitive materials (Fig. 6B), assuming that photope-riod sensitivity was expressed by the index variable for photoperiodsensitivity, which was equal to F (March)/F (July) as observed inSenegal. Consequently, photoperiod-sensitive genotypes appearedto respond less to altitude than photoperiod-insensitive genotypes.It thus appears that there is a linkage between the genotypic alti-tude effect on F and other genotypic phenology parameters, suchas earliness and photoperiod sensitivity.
		+
		+	[[File:IC4R006-Phenomics-2015-26104576-f6.png \|center \|thumb \|800px \|'''Fig. 6. Relationships between altitude effects on duration to flowering (difference high minus mid altitude) and other phenological traits for all genotypes pooled. (A) Altituderesponse vs. baseline duration at mid-altitude in Madagascar, with lines indicating linear regression line and 95% confidence interval; (B) index of photoperiod response inSenegal vs. altitude response in Madagascar.''']]

	==Labs working on this Project==		==Labs working on this Project==

← Older revision		Revision as of 17:02, 28 July 2016
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	[[File:IC4R006-Phenomics-2015-26104576-f1.png \|center \|thumb \|800px \|'''Fig. 1. Graph A: Weather variables averaged for the period from sowing to 80 d after sowing at the Senegal site. Tmax, Tmean, Tminare maximum, mean and minimum airtemperature at 2 m, respectively. RH is minimum daily relative air humidity. PET is potential evaporation according to FAO standard. The recommended sowing dates for thehot–dry season (HDS) and the wet season (WS) are indicated. Graph B: Astronomic day length at sowing''']]		[[File:IC4R006-Phenomics-2015-26104576-f1.png \|center \|thumb \|800px \|'''Fig. 1. Graph A: Weather variables averaged for the period from sowing to 80 d after sowing at the Senegal site. Tmax, Tmean, Tminare maximum, mean and minimum airtemperature at 2 m, respectively. RH is minimum daily relative air humidity. PET is potential evaporation according to FAO standard. The recommended sowing dates for thehot–dry season (HDS) and the wet season (WS) are indicated. Graph B: Astronomic day length at sowing''']]
		+
		+	* floweringSenegal. Only four check varieties were replicated for each ofthe 6 sowing dates in the augmented design of the experimentin Senegal. No block (replication) effects were observed accordingto ANOVA, whereas genotype, sowing date and date X genotypeeffects were highly significant (P < 0.0001) (Table 2A). Broad-senseheritability on the basis of family means was high at h2= 0.95(Table 2C).Madagascar. All 209 accessions were replicated in both yearsand locations. There was a significant block (replication) effecton time to flowering (P < 0.0001, F = 6.0) but it was negligiblein size as compared to the year (F = 156), location (F = 30783)and genotype (F = 367) effects, which were also highly significant(P < 0.0001) (Table 2B). Broad-sense heritability of time to floweringwas h2= 0.98 (Table 2C).
		+
		+	[[File:IC4R006-Phenomics-2015-26104576-f2.png \|center \|thumb \|800px \|'''Fig. 2. Duration from sowing to maximum flowering for four check genotypes. (A) Observations for 6 sowing dates in Senegal in 2009 (means and SEM for 6 replications).(B) Observations for Madagascar at mid altitude (857 m asl) and high altitude (1497 m asl) for 2009 and 2010 (means and SEM of 3 replications. The straight lines connectthe 2-year means for two altitudes. No data for cv. Chomrong were available for high altitude.''']]

	==Labs working on this Project==		==Labs working on this Project==

@@ Line 9: / Line 9: @@
 ==Research Findings==
-* The environmentsThe six sowing dates in Senegal subjected the crop to very differ-ent weather and day length conditions (Fig. 1). Weather variablesare presented in Fig. 1A as averages for the initial 80 d of the cropas a rough measure of conditions during pre-floral developmentstages. The first three sowing dates were associated with low min-imum air humidity (RHmin) averaging less than 30%, while meanminimum meanminimum temperature increased from 16.4 (February crop) to 19.0(April crop)℃. Mean and maximal temperatures increased at a sim-ilar rate, with a constant mean diurnal temperature amplitude ofabout 15℃.
+* The environmentsThe six sowing dates in Senegal subjected the crop to very differ-ent weather and day length conditions (Fig. 1). Weather variablesare presented in Fig. 1A as averages for the initial 80 d of the cropas a rough measure of conditions during pre-floral developmentstages. The first three sowing dates were associated with low min-imum air humidity (RHmin) averaging less than 30%, while meanminimum meanminimum temperature increased from 16.4 (February crop) to 19.0(April crop)℃. Mean and maximal temperatures increased at a sim-ilar rate, with a constant mean diurnal temperature amplitude ofabout 15℃. Astronomic day length varied between 11.05 h in winter and12.97 h in summer (wet season) (Fig. 1B). The July crop had thelongest days at sowing but experienced decreasing day lengththroughout its life cycle. Conversely, the February crop had theshortest days at sowing but experienced increasing day lengththroughout its cycle.
 ==Labs working on this Project==

← Older revision		Revision as of 15:30, 28 July 2016
Line 21:		Line 21:

	==Corresponding Author==		==Corresponding Author==
		+	* '''M. Dingkuhn''': m.dingkuhn@irri.org

@@ Line 3: / Line 3: @@
 ==The Background of This Project==
+* The GRiSP Global Rice Phenotyping Network seeks to assemble a multi-environment, multi-trait phe-nomics resource for rice (Oryza sativa L.) diversity panels in order to understand existing genetic diversityand identify genes/alleles conveying adaptation and yield potential. Phenology is central to plant adap-tation and productivity in different agro-ecologies.
 ==Plant Materials & Treatment==