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QTL Mapping of Low-Temperature Germination Ability in the Maize IBM Syn4 RIL Population.

Hu S, Lübberstedt T, Zhao G, Lee M - PLoS ONE (2016)

Bottom Line: It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage.The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively.The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.

View Article: PubMed Central - PubMed

Affiliation: The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Lin'an, 311300, Zhejiang, China.

ABSTRACT
Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16 h, 18°C/8 h) and optimum temperature (28°C/24 h) between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org). Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.

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Chromosomal location of quantitative trait loci (QTL) for germination ability under low and optimum temperature conditions in IBM Syn4 population.
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pone.0152795.g002: Chromosomal location of quantitative trait loci (QTL) for germination ability under low and optimum temperature conditions in IBM Syn4 population.

Mentions: The genotypic data (S2 Table) were retrieved from the MaizeGDB website (http://www.maizegdb.org/ancillary/qtl/ibm302cross.np). QTL were detected based on LOD thresholds after permutation tests. The LOD thresholds for optimum-temperature germination rate (OTGR) varied from 3.72 to 4.72. Only three QTL controlling OTGR were detected on chromosomes 5, 6, 7 (Table 2; Fig 2). These QTL explained 5.75–7.78% of the phenotypic variation. The LOD thresholds for low-temperature germination rate (LTGR) varied from 3.12 to 9.66. A total of six QTL controlling LTGR were detected on five chromosomes (Table 2; Fig 2). Of the six QTL, two QTL were located on chromosome 5, the other four QTL was located on chromosomes 4, 6, 7, and 9. These QTL explained 3.39–11.29% of the phenotypic variation. qLTGR5-1 had the highest LOD values and the highest contribution to phenotypic variance. The QTL region from B73 background had a positive effect on LTGR (Table 2). The LOD thresholds for low-temperature primary root length (LTPRL) varied from 3.33 to 6.66. A total of six QTL controlling LTPRL were detected on four chromosomes (Table 2; Fig 2). Of the six QTL, two QTL were located on chromosome 5, two QTL were located on chromosome 6, and the other two QTL were located on chromosomes 4 and 9. These QTL explained 3.96–8.41% of the phenotypic variation. qLTPRL9-1 had the highest LOD values and explained most of the phenotypic variation. The QTL region from the B73 background had a negative effect on LTPRL (Table 2).


QTL Mapping of Low-Temperature Germination Ability in the Maize IBM Syn4 RIL Population.

Hu S, Lübberstedt T, Zhao G, Lee M - PLoS ONE (2016)

Chromosomal location of quantitative trait loci (QTL) for germination ability under low and optimum temperature conditions in IBM Syn4 population.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4816396&req=5

pone.0152795.g002: Chromosomal location of quantitative trait loci (QTL) for germination ability under low and optimum temperature conditions in IBM Syn4 population.
Mentions: The genotypic data (S2 Table) were retrieved from the MaizeGDB website (http://www.maizegdb.org/ancillary/qtl/ibm302cross.np). QTL were detected based on LOD thresholds after permutation tests. The LOD thresholds for optimum-temperature germination rate (OTGR) varied from 3.72 to 4.72. Only three QTL controlling OTGR were detected on chromosomes 5, 6, 7 (Table 2; Fig 2). These QTL explained 5.75–7.78% of the phenotypic variation. The LOD thresholds for low-temperature germination rate (LTGR) varied from 3.12 to 9.66. A total of six QTL controlling LTGR were detected on five chromosomes (Table 2; Fig 2). Of the six QTL, two QTL were located on chromosome 5, the other four QTL was located on chromosomes 4, 6, 7, and 9. These QTL explained 3.39–11.29% of the phenotypic variation. qLTGR5-1 had the highest LOD values and the highest contribution to phenotypic variance. The QTL region from B73 background had a positive effect on LTGR (Table 2). The LOD thresholds for low-temperature primary root length (LTPRL) varied from 3.33 to 6.66. A total of six QTL controlling LTPRL were detected on four chromosomes (Table 2; Fig 2). Of the six QTL, two QTL were located on chromosome 5, two QTL were located on chromosome 6, and the other two QTL were located on chromosomes 4 and 9. These QTL explained 3.96–8.41% of the phenotypic variation. qLTPRL9-1 had the highest LOD values and explained most of the phenotypic variation. The QTL region from the B73 background had a negative effect on LTPRL (Table 2).

Bottom Line: It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage.The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively.The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.

View Article: PubMed Central - PubMed

Affiliation: The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Lin'an, 311300, Zhejiang, China.

ABSTRACT
Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16 h, 18°C/8 h) and optimum temperature (28°C/24 h) between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org). Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.

Show MeSH
Related in: MedlinePlus