Abstract
Seed germination and early seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice (DSR). To investigate the genetic mechanisms underlying seed germination and early seedling growth in rice, 275 recombinant inbred lines (RILs) were genotyped in this study via the genotyping-by-sequencing (GBS) approach to construct a high-density linkage bin map based on the parent-independent genotyping method. Quantitative trait loci (QTLs) for 12 traits related to seed germination and early seedling growth were analyzed. Totally, 22 additive loci were detected, after analysis of the interaction between additive QTLs and environments, five stable additive loci were obtained. Among them, loci 4, 5, 12 and 14 exhibited clear pleiotropic effects that were associated with multiple traits. Analysis of the effects of the five additive stable loci showed that a single locus increased the corresponding phenotypic value. Ten of the 275 RILs pyramided the excellent alleles of the five stable genetic loci. Most phenotypic values of the ten RILs were greater than the average values. Four RILs (G260, G342, G371, and G401) with more excellent phenotypic values were subsequently selected; these RILs could serve as donor parents of favorable alleles in the breeding process. Due to the existence of pleiotropy, the use of these genetic loci for pyramid breeding can further increase the efficiency to reach breeding goals. In addition, these five stable loci have an average physical interval of only 170 kb, we also further identified five promising candidate genes by qRT-PCR, which provides us with a basis for future cloning of these genes. Overall, this work will help broaden our understanding of the genetic control of seed germination and early seedling growth, and this study provides both a good theoretical basis and a new genetic resource for the breeding of direct-seeded rice.
Highlights
Rice (Oryza sativa L.) is one of the most important food crops worldwide
Continuous single-peak pattern distributions were observed for all 12 investigated traits, which is consistent with quantitative traits controlled by multiple genes (Table 1 and Figure 1)
Heritabilities for eight traits related to early seedling vigor had a relatively high heritability of 96.770-98.570%
Summary
Owing to its low cost and operational simplicity, the direct-seeding method of rice has become increasingly popular worldwide (Mahender et al, 2015). There are many factors limiting the growth and development of directly seeded rice (DSR), such as low emergence rates, difficulties with weeding, and population unevenness (Wang, 2009). QTLs for Seed Vigor in Rice are critical phases in rice growth and development. Uniform germination can significantly improve field emergence, and strong seedlings can improve the capability to compete against weeds at the seedling stage (Rao et al, 2007). The mining of key genes that control seed germination and seedling establishment to elucidate their underlying molecular mechanisms is an urgent and important objective in rice breeding
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