Haplotype Analysis of the GL7/GW7/SLG7 Gene and Its Application in Improving the Grain Quality of Three-Line Hybrid Rice

Abstract

Improving grain quality is second only to enhancing grain yield in breeding hybrid rice. Yet, rice grain quality, especially milling and appearance quality, is facing increasing threats from global warming due to climate change, leading to a relatively slow progress in high-quality rice breeding. Identifying additional grain quality genes is an effective way to combat against the threats on rice grain quality. In the present study, we used the germplasm from 3,000 Rice Genomes Project for genome-wide association study, and identified GL7/GW7/SLG7 as a major QTL besides GS3 and GW5 for grain shape. Among nine haplotypes of GL7 (H1-9), H1-H4, which harbored an 11-bp deletion, were designated as the functional GL7 allele and were primarily present in Geng/Japonica (GJ) rice. We developed KASP markers for GL7 major haplotypes (H1 and H2), and established a breeding system assisted by the markers to effectively improve Xian/Indica (XI) hybrids for grain quality. Yuehesimiao (YHSM) and Yixiang 1 A (YX1A) are widely applicated XI restorer line and sterile line in three-line hybrids. The improved hybrid YX1A^GL7/YHSM^GL7 exhibited longer grain, higher ratio of grain length-to-width and larger rate of head rice, but lower chalkiness rate and degree than that of any other hybrids and both parents. Furthermore, the improved hybrid with GL7 had statistically same yield of grains with all other hybrids, indicating no penalty of grain yield while improving grain quality. The GL7 haplotype along with its marker KASP-S2 and breeding strategy resulted from this study could be valuable sources for developing XI hybrids with high quality and high yield of grains in rice.

Keywords: GL7/GW7; Oryza sativa; Grain Quality; Hybrid Rice.

Fig. 1

Identification and haplotype analysis of GL7. a) Manhattan plots and b) quantile–quantile plots depicting GWAS results using a mixed model for grain length-to-width ratio in rice. c) Gene structure, d) haplotype analysis and e) phylogenetic analysis of GL7 in varieties from 3 K-RGP. Effects of GL7 allele (-) and gl7 allele (TATCACTTTCT, namely the 11-bp insertion) on grain length-to-width ratio in all varieties f) and the GJ group g). The variants in (d) named as S and ID represent SNP and InDels variations respectively, and those marked in red were used to design molecular markers

Fig. 2

MAS design of GL7 on improving three-line hybrid rice grain quality. a) The genotypes of major rice grain quality genes of tested parental lines. b) The fluorescence calling of effective GL7 KASP marker. Red, blue, and green dots represent homozygous GL7, homozygous gl7, and heterozygous genotypes, respectively. c) Molecular design breeding schedule of YHSM^GL7, YX1B^GL7 and YX1A^GL7

Fig. 3

Introducing of GL7 improved the grain quality of YHSM. a) The plant morphology of YHSM and YHSM^GL7 lines (scale bar = 20 cm). b) The genome sequence information of YHSM^GL7. The blue lines indicate the sequences introgressed into YHSM. c) The seed of morphology of YHSM and YHSM^GL7 lines (scale bars from left to right were 1 cm and 0.5 cm, respectively). d) The appearance of YHSM and YHSM^GL7 head rice (scale bar = 1 cm). e) The RVA properties of YHSM and YHSM^GL7 lines. The grain length f), grain width g), grain length-width ratio h), chalkiness rate i) and chalkiness degree j) of YHSM and YHSM^GL7 lines

Fig. 4

Introducing of GL7 improved the grain quality of YX1B. a) The plant morphology of YX1B and YX1B^GL7 lines (scale bar = 20 cm). b) The genome sequence information of YX1B^GL7. The blue lines indicate the sequences introgressed into YX1B. c) The seed of morphology of YX1B and YX1B^GL7 lines (scale bars from left to right were 1 cm and 0.5 cm, respectively). d) The appearance of YX1B and YX1B^GL7 head rice (scale bar = 1 cm). e) The RVA properties of YX1B and YX1B^GL7 lines. The grain length f), grain width g), grain length-width ratio h), chalkiness rate i) and chalkiness degree j) of YX1B and YX1B^GL7 lines

Fig. 5

Introducing of GL7 improved the grain quality of hybrid rice. The plant morphology a) (scale bar = 20 cm), panicle morphology b) (scale bar = 5 cm), seed morphology c) (scale bar = 1 cm in the left and 0.5 cm in the right), head rice appearance d) (scale bar = 1 cm) and RVA properties e) of YX1A/YHSM, YX1A/YHSM^GL7, YX1A^GL7/YHSM and YX1A^GL7/YHSM^GL7 hybrid lines. The histogram of grain length f), grain width g), grain length-width ratio h), chalkiness rate i) and chalkiness degree j) of YX1A/YHSM, YX1A/YHSM^GL7, YX1A^GL7/YHSM and YX1A^GL7/YHSM^GL7 hybrid lines