Computational protocol: Sequence Variation and Expression Analysis of Seed Dormancy- and Germination-Associated ABA- and GA-Related Genes in Rice Cultivars

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[…] We acquired sequences of seed dormancy- and germination-associated genes from Arabidopsis and rice databases (Goff et al., ; Yu et al., ). We analyzed ABA metabolism-related genes from rice Nipponbare including OsNCED1 (AY838897), OsNECD2 (AY838898), OsNCED3 (AY838899), OsNCED4 (AY838900), OsNCED5 (AY838901), OsCYP707A5 (AB277270), OsCYP707A6 (NM_001068556), OsCYP707A7 (NM_001069901), and OsGPCR (CM000147), and homologs from Arabidopsis including AtNCED1 (AT3G63520), AtNCED2 (AT4G18350), AtNCED3 (AT3G14440), AtNCED4 (AT4G19170), AtNCED5 (AT1G30100), AtNCED6 (AT3G24220), AtNCED9 (AT1G78390), AtCYP707A1 (AT4G19230), AtCYP707A2 (AT2G29090), AtCYP707A3 (AT5G45340), AtCYP707A4 (AT3G19270), and AtGCR2 (AT1G52920) (Note: not all NCED enzymes are involved in ABA biosynthesis in Arabidopsis). GA metabolism-related genes from rice are OsGA20ox1 (AC096690), OsGA20ox2 (NM_001051549), OsGA20ox3 (AP005840), OsGA20ox4 (NM_001062119), OsGA3ox1 (NM_001048721), OsGA3ox2 (AC144738), OsGA2ox1 (AC119288), OsGA2ox2 (NM_001048899), OsGA2ox3 (NM_001050827), OsGA2ox4 (AC132485), OsGA2ox5 (NM_001062846), and OsGID1 (AB211399), and homologs from Arabidopsis are AtGA20ox1 (At4g25420), AtGA20ox2 (At5g51810), AtGA20ox3 (At5g07200), AtGA3ox1 (At1g15550), AtGA3ox2 (At1g80340), AtGA3ox3 (At4g21690), AtGA2ox1 (AT1G78440), AtGA2ox2 (AT1G30040), AtGA2ox3 (AT2G34555), and AtGID1 (AT3G05120). Alignment of sequences and phylogenetic analysis were carried out by using ClustalW with default parameters and MEGA4.1 with neighbor-joining method (Tamura et al., ). All sequences of 9311, PA64s, and Nipponbare used in this study are provided in in Supplementary Material. For each gene pair, we calculated the number of non-synonymous substitutions per non-synonymous site (Ka) and the number of synonymous substitutions per synonymous site (Ks) using the maximum-likelihood method (Goldman and Yang, ). Ka/Ks = 1 indicates neutral evolution, where the number of non-synonymous changes at each possible non-synonymous site is the same as the number of synonymous changes per synonymous site. Ka/Ks < 1 suggests purifying selection, where selection generally eliminates deleterious mutations; Ka/Ks > 1 indicates positive selection, where selection bring more amino acid changes. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Oryza sativa
Chemicals Abscisic Acid