Fine mapping of interspecific secondary CSSL populations revealed key regulators for grain weight at qTGW3.1 locus from Oryza nivara

Abstract

Grain weight (GW) is the most important stable trait that directly contributes to crop yield in case of cereals. A total of 105 backcross introgression lines (BC₂F₁₀ BILs) derived from Swarna/O. nivara IRGC81848 (NPS) and 90 BILs from Swarna/O. nivara IRGC81832 (NPK) were evaluated for thousand-grain weight (TGW) across four years (wet seasons 2014, 2015, 2016 and 2018) and chromosome segment substitution lines (CSSLs) were selected. From significant pair- wise mean comparison with Swarna, a total of 77 positively and 29 negatively significant NPS lines and 62 positively and 29 negatively significant NPK lines were identified. In all 4 years, 14 NPS lines and 9 NPK lines were positively significant and one-line NPS69 (IET22161) was negatively significant for TGW over Swarna consistently. NPS lines and NPK lines were genotyped using 111 and 140 polymorphic SSRs respectively. Quantitative trait locus (QTL) mapping using ICIM v4.2 software showed 13 QTLs for TGW in NPS. Three major effect QTLs qTGW2.1, qTGW8.1 and qTGW11.1 were identified in NPS for two or more years with PVE ranging from 8 to 14%. Likewise, 10 QTLs were identified in NPK and including two major effect QTL qTGW3.1 and qTGW12.1 with 6 to 32% PVE. In all QTLs, O. nivara alleles increased TGW. These consistent QTLs are very suitable for fine mapping and functional analysis of grain weight. Further in this study, CSSLs NPS1 (10-2S) and NPK61 (158 K) with significantly higher grain weight than the recurrent parent, Swarna cv. Oryza sativa were selected from each population and secondary F₂ mapping populations were developed. Using Bulked Segregant QTL sequencing, a grain weight QTL, designated as qTGW3.1 was fine mapped from the cross between NPK61 and Swarna. This QTL explained 48% (logarithm of odds = 32.2) of the phenotypic variations and was fine mapped to a 31 kb interval using recombinant analysis. GRAS transcription factor gene (OS03go103400) involved in plant growth and development located at this genomic locus might be the candidate gene for qTGW3.1. The results of this study will help in further functional studies and improving the knowledge related to the molecular mechanism of grain weight in Oryza and lays a solid foundation for the breeding for high yield.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-024-01483-0.

Keywords: CSSLs; GBS; GRAS; Grain weight; Oryza nivara; QTLs.

Fig. 1

Breeding scheme used for developing mapping populations and further fine mapping of TGW QTLs in the study

Fig.2

Frequency distribution and boxplot diagrams of average thousand grain weight in the mapping populations used in this study i NPS, ii NPK, iii FNPS and iv FNPK

Fig. 3

Linkage map in cM (Kosambi, 1944) showing QTLs identified in BC₂F₈ Swarna/O. nivara IRGC81848 (NPS) population. QTLs identified in two or more years are indicated in bold

Fig. 4

Linkage map in cM (Kosambi, 1944) showing QTLs identified in BC₂F₈ Swarna/O. nivara IRGC81832 (NPK) population. QTLs identified in two or more years are indicated in bold

Fig. 5

Linkage map in cM (Kosambi, 1944) using both SSR and SNP genotypic data showing Fine mapping of qTGW3.1 QTL identified in Swarna/O. nivara IRGC81832 (NPK) population into a to 31 kb region harbouring Os03go103400