Breeding of High Cooking and Eating Quality in Rice by Marker-Assisted Backcrossing (MABc) Using KASP Markers

Abstract

The primary goals of rice breeding programs are grain quality and yield potential improvement. With the high demand for rice varieties of premium cooking and eating quality, we developed low-amylose content breeding lines crossed with Samgwang and Milkyqueen through the marker-assisted backcross (MABc) breeding program. Trait markers of the SSIIIa gene referring to low-amylose content were identified through an SNP mapping activity, and the markers were applied to select favorable lines for a foreground selection. To rapidly recover the genetic background of Samgwang (recurrent parent genome, RPG), 386 genome-wide markers were used to select BC1F1 and BC2F1 individuals. Seven BC2F1 lines with targeted traits were selected, and the genetic background recovery range varied within 97.4–99.1% of RPG. The amylose content of the selected BC2F2 grains ranged from 12.4–16.8%. We demonstrated the MABc using a trait and genome-wide markers, allowing us to efficiently select lines of a target trait and reduce the breeding cycle effectively. In addition, the BC2F2 lines confirmed by molecular markers in this study can be utilized as parental lines for subsequent breeding programs of high-quality rice for cooking and eating.

Genome-Wide Association Mapping of Mixed Linkage (1,3;1,4)-β-Glucan and Starch Contents in Rice Whole Grain

“…As reported by Moongngarm ( 2013 ), rice endosperm contains up to 70% of starch, which is not found in the cell wall itself. In other studies using a few samples, the starch content of rice milled grain was reported between 78.1 and 85.6% (Fujita et al, 2007 ) and 80 and 82% (Kim et al, 2021 ).…”

Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection

“…Simultaneously, the genetic basis of agronomic traits is also a scientific issue in determining crop promoting breeding programs (Pasam et al, 2012 ). In line with the two most commonly used methods in traits identification: (1) QTL mapping for crossed results (Skøt et al, 2005 ) and (2) association mapping between molecular markers and traits (Verdeprado et al, 2018 ), the breeding program is vital to identify the genes of interest for their efficient performance on agronomic traits (Kim M.-S. et al, 2021 ). A marker-assisted backcross selection employed by MABc was the most recent breeding method that not only potentially overcome conventional breeding limitations (Suh et al, 2013 ) but it can also speed up the genome recovery (99%) of recurrent-parent within three backcrosses (Miah et al, 2015 ).…”

“…A marker-assisted backcross selection employed by MABc was the most recent breeding method that not only potentially overcome conventional breeding limitations (Suh et al, 2013 ) but it can also speed up the genome recovery (99%) of recurrent-parent within three backcrosses (Miah et al, 2015 ). A recent successful MABc program for ECQ rice was introduced through the functioning of SSIIIa gene responsible for low-AC, and the breeding program was mainly performed based on the identified fSNP (G/A) located on exon 3 of SSIIIa gene (Kim M.-S. et al, 2021 ). For the waxy gene, some functional alleles have long been measured for their performances in ECQ-related breeding development: G/T (at splice site of intron 1) introgression in Chinese male sterile hybrid rice (LTF-A and ZS-A) (Liu et al, 2006 ) and CT 17 transfer into II-32B lines for its low-AC (Jin et al, 2010 ).…”

“…Various strategies, such as exploring wild rice germplasm and natural or artificial mutations, have also been employed by breeders to broaden the genetic diversity of rice (Shen et al, 2017 ). Recent research was performed on the breeding improvement of some ECQ Korean rice by marker-assisted backcrossing (MABc) markers [kompetitive allele-specific PCR markers (KASP)] (Kim M.-S. et al, 2021 ), the development of novel waxy alleles by CRISPR/Cas9 system for the improvement of fine-tuned AC rice (Huang et al, 2020 ), and CRISPR/Cas9-based editing of the waxy gene in a 5′ untranslated region- (UTR-) intron region for rice grain quality improvement (Zeng et al, 2020 ). Different selection methods for detecting genetic variations (alleles) were also increasing for their patterns or distinctive signatures and then determined signatures whether due to selection or other confounding effects such as bottlenecks, expansions, and subdivided populations (Sabeti et al, 2006 ).…”

Recent Advances in Rice Varietal Development for Durable Resistance to Biotic and Abiotic Stresses through Marker-Assisted Gene Pyramiding

“…The result of their study indicated that the RPG was 80.11% for BC 1 F 1 , 95.30% for BC 2 F 1 and 95.9% for BC 2 F 2 [58]. Recently, Kim et al [59] applied KASP markers in foreground and background selection to select rice lines with a high cooking and eating quality in each backcross generation. The results indicated that KASP markers were efficient in identifying BC 1 F 1 and BC 2 F 1 plants with a high cooking and eating quality and in quickly recovering the RPG.…”