Genetic Diversity and Phenotypic Variation in an Introgression Line Population Derived from an Interspecific Cross between Oryza glaberrima and Oryza sativa

Abstract

The introduction of closely related species genomic fragments is an effective way to enrich genetic diversity and creates new germplasms in crops. Here, we studied the genetic diversity of an introgression line (IL) population composed of 106 ILs derived from an interspecific tetra cross between O. glaberrima and O. sativa (RAM3/Jin23B//Jin23B///YuetaiB). The proportion of O. glaberrima genome (PGG) in the ILs ranged from 0.3% to 36.7%, with an average value of 12.32% which is close to the theoretically expected proportion. A total of 250 polymorphic alleles were amplified by 21 AFLP primer combinations with an average of 12 alleles per primer. Population structure analysis revealed that the IL population can be divided into four genetically distinct subpopulations. Both principal component analysis and neighbor-joining tree analysis showed that ILs with a higher PGG displayed greater genetic diversity. Canonical discriminant analysis identified six phenotypic traits (plant height, yield per plant, filled grain percentage, panicle length, panicle number and days to flowering) as the main discriminatory traits among the ILs and between the subpopulations and showed significant phenotypic distances between subpopulations. The effects of PGG on phenotypic traits in the ILs were estimated using a linear admixed model, which showed a significant positive effect on grain yield per plant (0.286±0.117), plant height (0.418 ± 0.132), panicle length (0.663 ± 0.107), and spikelet number per panicle (0.339 ± 0.128), and a significant negative effect on filled grain percentage (-0.267 ± 0.123) and days to flowering (-0.324 ± 0.075). We found that an intermediate range (10% − 20%) of PGG was more effective for producing ILs with favorable integrated agronomic traits. Our results confirm that construction of IL population carrying O. glaberrima genomic fragments could be an effective approach to increase the genetic diversity of O. sativa genome and an appropriate level of PGG could facilitate pyramiding more favorable genes for developing more adaptive and productive rice.

Identification and Functional Characterization of Two Major Loci Associated with Resistance against Brown Planthoppers (Nilaparvata lugens (Stål)) Derived from Oryza nivara

“…Miah et al [19] also reported the recurrent parent genome content in the selected BC 2 F 2 lines ranging from 92.7% to 97.7% using SSR markers. Chen et al [20], in their study of genetic diversity and phenotypic variation in an introgression line population of an interspecific Oryza glaberrima and Oryza sativa (RAM3/Jin23B//Jin23B///YuetaiB), revealed the proportion of the Oryza glaberrima genome (PGG) in the ILs ranging from 0.3% to 36.7%, with an average value of 12.32%.…”

Exploiting interspecific heterosis between African rice and Asian rice

“…The utilization of germplasm from relative species such as African rice is an effective way to broaden the GDs of rice (Chen et al., 2016). In this study, correlation analysis showed that PGG was positive correlated with GDs between the ILs and the test variety ST1, indicating that the introduction of African rice genomic fragments into Asian rice genome could effectively increase the GD of parents of PIHs.…”

“…Our previous studies showed that the introduction of African rice genomic fragments into genomes of Asian rice could induce great heterosis of yield‐related traits in PIHs, which were generated by crosses between the ILs and indica rice cultivars, and the optimal PGG for different ILs was estimated to be 10–20% and 15–30% for hybrid rice breeding purpose respectively, i.e. the PGG in these ranges may be optimal between gaining positive effect of broadening the GD and avoiding negative effect of introducing unfavorable genes such as interspecific sterility loci (Adedze et al., 2016; Chen et al., 2016).…”

“…The NERICA rice varieties were successfully developed from the interspecific crosses between the two species by using in vitro embryo rescue techniques at WARDA (Bimpong et al., 2010). The ILs derived from the interspecific crosses between the two species were also developed and used in research of mining new beneficial genes and breeding new types of elite inbred and hybrid rice varieties (Chen et al., 2016; Huang et al., 2013; Nassirou et al., 2017). Introgression lines incorporated with high proportions of African rice genomic fragments and their test crosses with Asian rice varieties usually showed low pollen and spikelet fertility, which limited the potential of the interspecific heterosis (Adedze et al., 2016; Chen et al., 2016; Xu et al., 2005).…”

“…Introgression lines (ILs) (Juan et al., 2015; Tian et al., 2006) and CSSLs (Liu et al., 2009; Zeng, Akshay, Liu, & Zhang, 2006) were developed, such as introducing chromosomal segments of different wild rice species into the Asian rice genome (Deng et al., 2012; Guo et al., 2013; Yuan et al., 2009). The introduction of African rice genomic fragments into the Asian rice to develop introgression restorer lines (IRLs) was also an effective way to broaden the genetic diversity and develop high‐yielding partial interspecific hybrid (PIH) rice incorporated with both intraspecific and interspecific heterotic loci (Adedze et al., 2016; Chen et al., 2016; Nassirou et al., 2017).…”