Identification of QTL TGW12 responsible for grain weight in rice based on recombinant inbred line population crossed by wild rice (Oryza minuta) introgression line K1561 and indica rice G1025

Abstract

Background: Limited genetic resource in the cultivated rice may hinder further yield improvement. Some valuable genes that contribute to rice yield may be lost or lacked in the cultivated rice. Identification of the quantitative trait locus (QTL) for yield-related traits such as thousand-grain weight (TGW) from wild rice speices is desired for rice yield improvement.

Results: In this study, sixteen TGW QTL were identified from a recombinant inbred line (RIL) population derived from the cross between the introgression line K1561 of Oryza minuta and the rice cultivar G1025. TGW12, One of most effective QTL was mapped to the region of 204.12 kb between the marker 2,768,345 and marker 2,853,491 of the specific locus amplified fragment (SLAF). The origin of TGW12 was tested using three markers nearby or within the TGW12 region, but not clarified yet. Our data indicated thirty-two open reading fragments (ORFs) were present in the region. RT-PCR analysis and sequence alignment showed that the coding domain sequences of ORF12, one MADS-box gene, in G1025 and K1561 were different due to alternative slicing, which caused premature transcription termination. The MADS-box gene was considered as a candidate of TGW12.

Conclusion: The effective QTL, TGW12, was mapped to a segment of 204.12 kb using RILs population and a MADS-box gene was identified among several candidate genes in the segment. The region of TGW12 should be further narrowed and creation of transgenic lines will reveal the gene function. TGW12 could be applied for improvement of TGW in breeding program.

Keywords: Introgression lines; SLAF; SSR; Transcription factor; Wild rice.

Fig. 1

Phenotypic evaluation of thousand-grain weight (TGW) for G1025, K1561 and RILs. The Y axis represents the number of RIL lines. The X axis represents the values of TGW: 16 g < TGW ≤ 20 g; 20 < TGW ≤ 22 g; 22 g < TGW ≤ 24 g; 24 g < TGW ≤ 26 g; 26 g < TGW ≤ 28 g; 28 g < TGW ≤ 30 g; TGW > 30 g. G1025 and K1501 are the parents with light and weight TGW, respectively. The arrows indicate the TGW range of the parents (G1025 and K1561), respectively

Fig. 2

Mapping of TGW12 by SSR and SLAF Markers

Fig. 3

Identification of QTLs for TGW. TGW12 were identified in 2015NN (A), 2016NN (B), and 2016WH (C), which was linked with Marker2768345

Fig. 4

Genotypes and phenotypes of 16 RILs and parents. Left figure, genotypes of 16 RILs and parents. Marker1–21, Marker2804825, Marker2755190, Marker272486, RM27748, Marker2758610, Marker2776377, Marker2832175, Marker2745315, Marker2853491, Marker2768345, Marker2764694, Marker2737811, Marker2797863, RM27638, Marker2734798, Marker2854577, Marker2827288, Marker2753963, Marker2716467, Marker2852418, Marker2816785, respectively. Solid bar represents segments of G1025, and hallow bar represents segments of K1561. Right figure, phenotypes of 13 RILs and parents

Fig. 5

Identification of TGW12 segment by SSR or SLAF markers. Lanes1–4, K1561, IR24, O. minuta, G1025. M, DNA marker 2000 plus

Fig. 6

RT-PCR for ORF12 and sequence alignment. a RT-PCR for ORF12. M, DNA marker 2000 plus; R, root; S, stem; L, leave; SAM, shoot apical meristem; YP, young panicles (1–5 cm); MP, mature panicles (15–20 cm). b Genomic structure of ORF12. Solid bar, exon; hollow bar, 3’untranslated region; line, intron; fold lines, alternative splicing. c the cDNA sequence alignment of ORF12 between G1025 and K1561. The red and green letters indicated the sequence of exon1, and the sequence showed in green letters are those kept in the cDNA of G1025 but spliced in K1561; the blue letters indicated the sequence of exon2; the black letters indicated the sequence of intron. The symbol of “\\” indicated the omitted sequences