Identification and Pyramiding of QTLs for Rice Grain Size Based on Short-Wide Grain CSSL-Z563 and Fine-Mapping of qGL3–2

Abstract

Background Chromosome segment substitution lines (CSSLs) can be used to dissect complex traits, from which single-segment substitution lines (SSSLs) containing a target quantitative trait loci (QTL) can be developed, and they are thus important for functional analysis and molecular breeding. Results A rice line with short wide grains, CSSL-Z563, was isolated from advanced-generation backcross population (BC3F6) derived from ‘Xihui 18’ (the recipient parent) and ‘Huhan 3’ (the donor parent). Z563 carried seven segments from ‘Huhan 3’, distributed on chromosomes 3, 7, and 8, with average substitution length of 5.52 Mb. Eleven QTLs for grain size were identified using secondary F2 population of ‘Xihui 18’/Z563. The QTLs qGL3–1, qGL3–2, and qGL7 control grain length in Z563 and have additive effects to reduce grain length; qGW3–1 and qGW3–2 control grain width in Z563 and have additive effects to increase grain width. Four SSSLs, three double-segment substitution lines (D1–D3), and two triple-segment substitution lines (T1 and T2) were developed containing the target QTLs. The genetic stability of eight QTLs, including qGL3–2, qGL3–1, and qGL7, was verified by the SSSLs. D1 (containing qGL3–2 and qGL3–1), D2 (qGL3–1 and qGL7), and T1 (qGL3–2, qGL3–1, and qGL7) had positive epistatic effects on grain length, and their grain length was shorter than that of the corresponding SSSLs. The QTL qGL3–2 was fine-mapped to a 696 Kb region of chromosome 3 containing five candidate genes that differed between ‘Xihui 18’ and Z563. These results are important for functional research on qGL3–2 and molecular breeding of hybrid rice cultivars. Conclusions The short and wide grain of Z563 was mainly controlled by qGL3–1, qGL3–2, qGL7, qGW3–1 and qGW3–2. The major QTL qGL3–2 was fine-mapped to a 696 Kb region of chromosome 3 containing five candidate genes. Different QTLs pyramiding displayed various phenotypes. In essence, the performance after pyramiding of genes depended on the comparison between the algebraic sum of the additive and epistatic effects of QTLs in the pyramidal line and the additive effect value of the single QTL. The results lay good foundation in the functional analysis of qGL3–2 and molecular design breeding of novel hybrid rice cultivars.

Identification and Pyramid of QTLs Based on Rice Short-wide Grain CSSL-Z414, SSSL, DSSL and Candidate Gene Analysis of qGL11 and qGW5

“…Zhang et al (2020) showed that pyramid of qGL5 (a=0.30) and qGL6 (a=0.13) produced longer grains (G=0.74) of D2 than S2 and S3 at the genetic backgrounds of Nipponbare. Liang et al (2021) argued that pyramiding of different QTLs produces different epistatic interaction and their performance after pyramiding depends on the comparison between the algebraic sum of additive and epistatic effects of QTLs in the pyramidal line and the additive effect of all single QTLs. On the basis of the rule, so long as knowing the additive effects and epistatic effects of target QTLs at the speci c environment, the phenotype of novel pyramided genotypes at speci c environment can be predicted and then suitable genotypes can be selected according to our breeding goal, thus realizing the concept of design breeding.…”

“…D2 harbored both qGL3, qGL11 and qCD3 and displayed shorter grain and lower chalkiness degree. Lower chalkiness degree is one of very important factors affected rice grain quality (Yang et al 2021) and different grain size are import to meet the requirement of various people's preferences (Feng et al 2021;Liang et al 2021). Thus, some secondary substitution lines with signi cantly lower chalkiness degree than Xihui 18, such as S1 and D1 are potential to be directly used as novel rice restorer lines to match with sterile lines.…”

QTL Analysis Based on A Rice Short-Wide Grain CSSL-Z414 and Substitution Mapping of qGL11 and qGW5

“…Lower chalkiness degree is a very important factor affecting rice grain quality (Yang et al 2021). Again, different grain sizes are import to meet the requirement of various people's preferences (Feng et al 2021;Liang et al 2021). Thus, these four SSSLs are potential to be directly used as novel rice restorer lines to breed novel hybrid rice varieties.…”

“…We also took the half of the difference of phenotype value into account as caused by inheritance. Thus, the epistatic effects between non-allele QTLs were estimated as half of the mean phenotypic values of (Xihui18+DSSL ij )-(SSSL i +SSSL j ) (Liang et al 2021). Finally, we used IBM SPSS Statistics 25.0 to conduct multiple comparison for all SSSLs and DSSLs as well as Xihui18.…”

“…When multiple substitution segments in SSSLs with target trait overlapped, the QTL was located in the overlapping region (Yang et al 2021). The additive effect of the QTL was calculated as half the difference between the mean phenotypic values of SSSL and Xihui18 (Liang et al, 2021). Within the maximum substitution intervals, we predicted the candidate gene information and combined with gene annotations to screen the possible candidate genes of qGL11 and qGW5 by the Gramene (http:/www.gramene.org/) and the Rice Annotation Project Data-base (https:/rapdb.dna.affrc.go.jp/) and the China National Rice Database Center (http:/www.ricedata.cn/).…”