Mapping and introgression of QTL for yield and related traits in two backcross populations derived from Oryza sativa cv. Swarna and two accessions of O. nivara

Abstract

Advanced backcross QTL (AB-QTL) analysis was carried out in two Oryza nivara-derived BC2F2 populations. For nine traits, we identified 28 QTL in population 1 and 26 QTL in population 2. The two most significant yield-enhancing QTL, yldp9.1 and yldp2.1 showed an additive effect of 16 and 7 g per plant in population 1, while yld2.1 and yld11.1 showed an additive effect of 11 and 10 g per plant in population 2. At least one O. nivara-derived QTL with a phenotypic variance of >15% was detected for seven traits in population 1 and three traits in population 2. The O. nivara-derived QTL ph1.1, nt12.1, nsp1.1, nfg1.1, bm11.1, yld2.1 and yld11.1 were conserved at the same chromosomal locations in both populations. Two major QTL clusters were detected at the marker intervals RM488-RM431 and RM6-RM535 on chromosomes 1 and 2, respectively. The colocation of O. nivara-derived yield QTL with yield meta-QTL on chromosomes 1, 2 and 9 indicates their accuracy and consistency. The major-effect QTL reported in this study are useful for marker-assisted breeding and are also suitable for further fine mapping and candidate gene identification.

Analysis of QTLs for panicle exsertion and its relationship with yield and yield-related traits in rice (Oryza sativa L.)

“…Thus, these loci are worthy for use when improving grain size and weight of 'Kasalath', and other rice varieties with small grain size, by marker-assisted selection and are also important in QTL pyramiding programs. The results of these pleiotropic QTLs are consistent with the corresponding traits reported in previous publications (Swamy et al, 2014).…”

“…The negative relationship between PE and GW may suggest that lower grain yield is directly derived from the scarcity of SNP companied by a longer PE. Previous studies have found several QTLs for highly correlated traits located on the same or on neighboring chromosomal intervals, possibly resulting from pleiotropism or multigenic effects (Marathi et al, 2012;Swamy et al, 2014). In the present study, four QTL clusters were located on four intervals: RM5389-RM6407, RM1347-RM341, RM6080-RM6832, and RM3628-RM412 on chromosomes 1, 2, 3, and 6, respectively (Figure 2).…”

Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing

“…Thus, some agronomically important traits of O. nivara are more similar to those of cultivated rice49. In a previous study, several significant yield-enhancing QTLs from O. nivara were identified by advanced backcross (BC 2 F 2 ) QTL analysis21. In the present study, by combining a high-density bin map with phenotypic data from ILs, O .…”

“…Some valuable genes from O . nivara , such as those for yield components, grain quality, and grassy stunt virus resistance have been transferred into cultivated rice and widely employed in rice production2021454647. However, owing to the overall inferior performance of O .…”

“…Many O. rufipogon introgression lines (ILs) have been developed by repeated selfing of advanced backcross populations and provide ideal genetic materials for evaluating agronomic traits and for positional cloning of interesting genes or QTLs, because of the simple and stable genetic background of wild rice ILs1415161718. The annual diploid species O. nivara is another close wild relative of cultivated rice with great potential to improve elite cultivars, for instance, enhanced grassy stunt virus resistance and yield components has been achieved through transferring useful genes from O. nivara into cultivated rice varieties192021. However, only few introgression libraries have been developed with O. nivara .…”