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Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci.

Dixit S, Grondin A, Lee CR, Henry A, Olds TM, Kumar A - BMC Genet. (2015)

Bottom Line: Rice requires better adaptation across a wide range of environments and cultivation practices to adjust to climate change.This study provides a wider picture of the genetics and physiology of adaptation of rice to wide range of environments.With a complete understanding of the processes and relationships between traits and trait groups, marker-assisted breeding can be used more efficiently to develop plant types that can combine all or most of the beneficial traits and show high stability across environments, ecosystems, and cultivation practices.

View Article: PubMed Central - PubMed

Affiliation: International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines. s.dixit@irri.org.

ABSTRACT

Background: Interaction and genetic control for traits influencing the adaptation of the rice crop to varying environments was studied in a mapping population derived from parents (Moroberekan and Swarna) contrasting for drought tolerance, yield potential, lodging resistance, and adaptation to dry direct seeding. A BC2F3-derived mapping population for traits related to these four trait groups was phenotyped to understand the interactions among traits and to map and align QTLs using composite interval mapping (CIM). The study also aimed to identify QTLs for the four trait groups as composite traits using multivariate least square interval mapping (MLSIM) to further understand the genetic control of these traits.

Results: Significant correlations between drought- and yield-related traits at seedling and reproductive stages respectively with traits for adaptation to dry direct-seeded conditions were observed. CIM and MLSIM methods were applied to identify QTLs for univariate and composite traits. QTL clusters showing alignment of QTLs for several traits within and across trait groups were detected at chromosomes 3, 4, and 7 through CIM. The largest number of QTLs related to traits belonging to all four trait groups were identified on chromosome 3 close to the qDTY 3.2 locus. These included QTLs for traits such as bleeding rate, shoot biomass, stem strength, and spikelet fertility. Multivariate QTLs were identified at loci supported by univariate QTLs such as on chromosomes 3 and 4 as well as at distinctly different loci on chromosome 8 which were undetected through CIM.

Conclusion: Rice requires better adaptation across a wide range of environments and cultivation practices to adjust to climate change. Understanding the genetics and trade-offs related to each of these environments and cultivation practices thus becomes highly important to develop varieties with stability of yield across them. This study provides a wider picture of the genetics and physiology of adaptation of rice to wide range of environments. With a complete understanding of the processes and relationships between traits and trait groups, marker-assisted breeding can be used more efficiently to develop plant types that can combine all or most of the beneficial traits and show high stability across environments, ecosystems, and cultivation practices.

No MeSH data available.


Related in: MedlinePlus

Percentage of traits showing significant variation in ANOVA across the four trait groups
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Fig2: Percentage of traits showing significant variation in ANOVA across the four trait groups

Mentions: The phenotypic variation among the parents was transferred to the progeny and significant genetic variation for a large proportion of traits studied under each trait group was observed. Significant differences among the progeny for 64–100 % of the traits were observed for the different trait groups (Fig. 2). Additional files 2, 3, 4 and 5 present the results of the analysis of variance (ANOVA) conducted for all experiments. In the three experiments conducted under lowland drought, a higher yield decline for parents and progenies was observed in Experiment 1A as compared to 1B and 1C. The progenies showed significant variation for all traits except for Normalized Difference Vegetation Index (NDVI), reduction of NDVI, root mass density, and percentage deep roots for which consistency in significance was not observed across the three maturity groups (Additional file 2). The progeny means ranged between the parent means or were equal to one of the parents for most traits except for some traits such as bleeding rate (in Experiment 1A and 1B), root mass density at 15–30 cm (in Experiment 1A), and days to flowering (in the three experiments). Under well-watered lowland conditions (Experiment 2), significant variation for all traits except spikelet fertility was observed (Additional file 3). The specificity of significance of variation for spikelet fertility under drought stress showed the higher level of tolerance to drought of Moroberekan over Swarna. Similar to the stress conditions, the progeny mean of the majority of the traits ranged between the two parents or were equal to one of the parents with the exception of days to flowering which stayed lower than both parents (Additional file 3). For lodging-related traits, significant differences were observed for all traits under both lowland and upland well-watered conditions (Additional files 3 and 4). The progeny means were intermediate for traits such as plant height, stem diameter, and stem strength with Moroberekan on the higher and Swarna on the lower side. These three traits played a crucial role in determining the resistance to lodging of the progeny with dwarf plant stature, larger stem diameter, and higher stem strength leading to higher resistance to lodging. The population was also screened under upland dry direct-seeded conditions to determine their adaptation to direct seeding (Experiments 3 and 4). Under well-watered upland conditions, significant variations for all traits except spikelet fertility were observed (Additional file 4). However, under seedling stage drought conditions, significant differences for early and uniform establishment were not observed (Additional file 5).Fig. 2


Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci.

Dixit S, Grondin A, Lee CR, Henry A, Olds TM, Kumar A - BMC Genet. (2015)

Percentage of traits showing significant variation in ANOVA across the four trait groups
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4526302&req=5

Fig2: Percentage of traits showing significant variation in ANOVA across the four trait groups
Mentions: The phenotypic variation among the parents was transferred to the progeny and significant genetic variation for a large proportion of traits studied under each trait group was observed. Significant differences among the progeny for 64–100 % of the traits were observed for the different trait groups (Fig. 2). Additional files 2, 3, 4 and 5 present the results of the analysis of variance (ANOVA) conducted for all experiments. In the three experiments conducted under lowland drought, a higher yield decline for parents and progenies was observed in Experiment 1A as compared to 1B and 1C. The progenies showed significant variation for all traits except for Normalized Difference Vegetation Index (NDVI), reduction of NDVI, root mass density, and percentage deep roots for which consistency in significance was not observed across the three maturity groups (Additional file 2). The progeny means ranged between the parent means or were equal to one of the parents for most traits except for some traits such as bleeding rate (in Experiment 1A and 1B), root mass density at 15–30 cm (in Experiment 1A), and days to flowering (in the three experiments). Under well-watered lowland conditions (Experiment 2), significant variation for all traits except spikelet fertility was observed (Additional file 3). The specificity of significance of variation for spikelet fertility under drought stress showed the higher level of tolerance to drought of Moroberekan over Swarna. Similar to the stress conditions, the progeny mean of the majority of the traits ranged between the two parents or were equal to one of the parents with the exception of days to flowering which stayed lower than both parents (Additional file 3). For lodging-related traits, significant differences were observed for all traits under both lowland and upland well-watered conditions (Additional files 3 and 4). The progeny means were intermediate for traits such as plant height, stem diameter, and stem strength with Moroberekan on the higher and Swarna on the lower side. These three traits played a crucial role in determining the resistance to lodging of the progeny with dwarf plant stature, larger stem diameter, and higher stem strength leading to higher resistance to lodging. The population was also screened under upland dry direct-seeded conditions to determine their adaptation to direct seeding (Experiments 3 and 4). Under well-watered upland conditions, significant variations for all traits except spikelet fertility were observed (Additional file 4). However, under seedling stage drought conditions, significant differences for early and uniform establishment were not observed (Additional file 5).Fig. 2

Bottom Line: Rice requires better adaptation across a wide range of environments and cultivation practices to adjust to climate change.This study provides a wider picture of the genetics and physiology of adaptation of rice to wide range of environments.With a complete understanding of the processes and relationships between traits and trait groups, marker-assisted breeding can be used more efficiently to develop plant types that can combine all or most of the beneficial traits and show high stability across environments, ecosystems, and cultivation practices.

View Article: PubMed Central - PubMed

Affiliation: International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines. s.dixit@irri.org.

ABSTRACT

Background: Interaction and genetic control for traits influencing the adaptation of the rice crop to varying environments was studied in a mapping population derived from parents (Moroberekan and Swarna) contrasting for drought tolerance, yield potential, lodging resistance, and adaptation to dry direct seeding. A BC2F3-derived mapping population for traits related to these four trait groups was phenotyped to understand the interactions among traits and to map and align QTLs using composite interval mapping (CIM). The study also aimed to identify QTLs for the four trait groups as composite traits using multivariate least square interval mapping (MLSIM) to further understand the genetic control of these traits.

Results: Significant correlations between drought- and yield-related traits at seedling and reproductive stages respectively with traits for adaptation to dry direct-seeded conditions were observed. CIM and MLSIM methods were applied to identify QTLs for univariate and composite traits. QTL clusters showing alignment of QTLs for several traits within and across trait groups were detected at chromosomes 3, 4, and 7 through CIM. The largest number of QTLs related to traits belonging to all four trait groups were identified on chromosome 3 close to the qDTY 3.2 locus. These included QTLs for traits such as bleeding rate, shoot biomass, stem strength, and spikelet fertility. Multivariate QTLs were identified at loci supported by univariate QTLs such as on chromosomes 3 and 4 as well as at distinctly different loci on chromosome 8 which were undetected through CIM.

Conclusion: Rice requires better adaptation across a wide range of environments and cultivation practices to adjust to climate change. Understanding the genetics and trade-offs related to each of these environments and cultivation practices thus becomes highly important to develop varieties with stability of yield across them. This study provides a wider picture of the genetics and physiology of adaptation of rice to wide range of environments. With a complete understanding of the processes and relationships between traits and trait groups, marker-assisted breeding can be used more efficiently to develop plant types that can combine all or most of the beneficial traits and show high stability across environments, ecosystems, and cultivation practices.

No MeSH data available.


Related in: MedlinePlus