Identification, pyramid, and candidate gene of QTL for yield-related traits based on rice CSSLs in Xihui18 background.

Unlabelled: Chromosome segment substitution line (CSSL) is important for functional analysis and design breeding of target genes. Here, a novel rice CSSL-Z431 was identified from restorer line Xihui18 as recipient and Huhan3 as donor. Z431 contained six segments from Huhan3, with average substitution length of 2.12 Mb. Compared with Xihui18, Z431 increased panicle number per plant (PN) and displayed short-wide grains. The short-wide grain of Z431 was caused by decreased length and increased width of glume cell. Then, thirteen QTLs were identified in secondary F population from Xihui18/Z431. Again, eleven QTLs () were validated by six single-segment substitution lines (SSSLs, S1-S6) developed in F. In addition, fifteen QTLs () were detected by these SSSLs, while not be identified in the F population. Multiple panicles of Z431 were controlled by and . should be the candidate gene for . The short-wide grain of Z431 was controlled by , etc. By DNA sequencing and qRT-PCR analysis, two best candidate genes for and were identified, respectively. In addition, pyramid of different QTLs in D1-D3 and T1-T2 showed independent inheritance or various epistatic effects. So, it is necessary to understand all genetic effects of target QTLs for designing breeding. Furthermore, these secondary substitution lines improved the deficiencies of Xihui18 to some extent, especially increasing yield per plant in S1, S3, S5, D1-D3, T1, and T2.

Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01284-x.