Substitution mapping of QTLs controlling seed dormancy using single segment substitution lines derived from multiple cultivated rice donors in seven cropping seasons

Abstract

A permanent advanced population containing 388 SSSLs was used for genetic analysis of seed dormancy; 25 QTLs including eight stable, six major and five new were identified. Seed dormancy (SD) is not only a complex biological phenomenon, but also a key practical problem in agricultural production closely related with pre-harvest sprouting (PHS). However, the genetic mechanisms of SD remain elusive. Here, we report the genetic dissection of SD in rice using 388 single segment substitution lines (SSSLs) derived from 16 donor parents. Continuous variation and positive correlations in seed germination percentages were observed in seven seasons. Genetic analysis revealed the narrow sense heritability in different seasons varied from 31.4 to 82.2% with an average value of 56.8%. In addition, 49 SSSLs exhibited significant difference to recipient parent HJX74 on SD in at least two seasons, and 12 of them were stably identified with putative QTLs in all of their corresponding cropping seasons. Based on substitution mapping, a total of 25 dormancy QTLs were detected on 11 chromosomes except the chromosome 5 with an interval length of 1.1 to 31.3 cM. The additive effects of these QTLs changed from -0.31 to -0.13, and the additive effect contributions ranged from 16.7 to 41.4%. Six QTLs, qSD3-2, qSD4-1, qSD7-1, qSD7-2, qSD7-3 and qSD11-2, showed large additive effect contributions (≥30%). Five QTLs, qSD3-3, qSD7-1, qSD7-4, qSD9-1 and qSD10-1, may represent novel ones. Furthermore, linkage and recombinant analysis delimited qSD7-1 to a locus 1.5 cM away from marker Oi2 and a 355-kb fragment flanked by RM1134 and Ui159, respectively. Taken together, this work conducts a comprehensive genetic dissection of SD and will provide more selections for breeding elite PHS-resistant rice varieties.

Analysis of QTLs on heading date based on single segment substitution lines in rice (Oryza Sativa L.)

“…Subsequently, the large-scale QTL identifications have been done for almost all interesting traits using these SSSLs 14–16 . Meanwhile, some SSSLs were selected as experimental materials to develop secondary populations such as F2 for QTL fine mapping and to aggregate SSSLs for epistatic analysis 8,17–22 and design breeding 14 .…”

QTL epistatic analysis for yield components with single‐segment substitution lines in rice

“…According to the three steps in it, (i) mapping loci involved in almost agronomically relevant traits; (ii) assessment of the allelic variations at those loci; and (iii) breeding by design, our laboratory had made rewarding works to try breeding by design. We constructed a platform including 1,529 single‐segment substitution lines (SSSLs), and then used these SSSLs for conducting quantitative trait loci (QTL) analysis (Chen et al., ; Liu, Zhu, Zhang, Li, & Ye, ; Wang et al., , ; Ying et al., ; Zhao, Zhu, Zeng, Zhang, & Xu, ; Zhou et al., ; Zhu et al., ) and attempted to pyramid breeding (Dai et al. ; Dai et al., 2016).…”

Breeding by design of CMS lines on the platform of SSSL library in rice

“…To date, more than 2000 SSSLs were developed, in which a rich of genes from AA genome of the Oryza genus was collected (He et al 2005;Xi et al 2006;He et al 2017;Zhao et al 2019). At the second step, we detected the genotypes on the chromosomal substituted segments in the SSSLs by mapping of genes or QTLs of important traits (He et al 2005;Zhao et al 2007;Liu et al 2010;Zhang et al 2012;Naeem et al 2013;Yang et al 2016;Zhou et al 2017;Zhu et al 2018), by assessing allelic variations at the loci of interest (Zeng et al 2006;Teng et al 2012;Cai et al 2013), by analyzing interaction of gene by gene and gene by environment (Liu et al 2008;Liu et al 2012;Chen et al 2014;Qin et al 2015;Zhao et al 2016;Yang et al 2018), and by cloning genes of agronomic important (Wang et al 2012;Wang et al 2015). A large gene information has been collected from the SSSL library.…”

“…The genes for agronomic importance on the substituted segments in the SSSLs were analyzed. The gene information was collected including gene location, allelic variation, interaction of gene by gene and gene by environment, molecular function, and so on (Zeng et al 2006;Zhao et al 2007;Liu et al 2008;Liu et al 2010;Liu et al 2012;Teng et al 2012;Wang et al 2012;Zhang et al 2012;Chen et al 2014;Qin et al 2015;Wang et al 2015;Yang et al 2016;Zhao et al 2016;Zhou et al 2017;Yang et al 2018;Zhu et al 2018). To assess allelic variations at the Rf3 and Rf4 loci, the SSSLs carrying one of the loci in the substituted segments were selected from the library.…”