The anaerobic germination 1 (AG1) locus, which confers tolerance to the anaerobic germination of rice seed, has been previously identified and a gel-based InDel DNA marker developed for marker-assisted selection (MAS). However, there is a need for marker development for high-throughput genotyping in order to increase the breeding efficiency. Single nucleotide polymorphisms (SNPs)-based Kompetitive Allele Specific PCR (KASP) markers enable high-accuracy and high-throughput analyses for the genotyping of AG1 locus. In the present study, we developed one AG1 InDel-specific and four flanking KASP markers, which can be used as the foreground and recombination markers, respectively, for the AG1 locus. Of those, three KASP markers developed were validated with Dasan-AG1 (BC₃F₂) segregating lines; the AG1 InDel-specific KASP marker was 100% consistent with the existing AG1 gel-based marker, while the two flanking markers showed 70.3 and 66.7 percent consistency to the AG1 gel-based marker, respectively. In addition, the five KASP markers developed were further used to genotype 78 Korean and 95 foreign rice varieties. The genotyping results with 172 varieties revealed that most of the Korean varieties possessed the AG1 locus; however, a wide variation was observed in the foreign varieties for AG1 locus. Hence, the KASP markers developed for AG1 locus show promise as useful tools for expediting the breeding of varieties tolerant to anaerobic germination stress via high-throughput genotyping.

Citations

Citations to this article as recorded by  

• KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance
  Bhawna Dipta, Salej Sood, Vikas Mangal, Vinay Bhardwaj, Ajay Kumar Thakur, Vinod Kumar, Brajesh Singh
  Molecular Biology Reports.2024;[Epub]     CrossRef
• Development and Validation of Kompetitive Allele-Specific Polymerase Chain Reaction Markers for Seed Protein Content in Soybean
  Shuangzhe Li, Chenyijun Guo, Xuezhen Feng, Jing Wang, Wenjing Pan, Chang Xu, Siming Wei, Xue Han, Mingliang Yang, Qingshan Chen, Jinxing Wang, Limin Hu, Zhaoming Qi
  Plants.2024; 13(24): 3485.     CrossRef
• KASP mapping of QTLs for yield components using a RIL population in Basmati rice (Oryza sativa L.)
  Hamza Ashfaq, Reena Rani, Naila Perveen, Allah Ditta Babar, Umer Maqsood, Muhammad Asif, Katherine A. Steele, Muhammad Arif
  Euphytica.2023;[Epub]     CrossRef
• Development of SNP Marker Set to Select Varieties Tolerant to Multiple Abiotic Stresses in Rice
  Jung-Woo Lee, Jung-Seok Oh, Soo-Cheul Yoo
  Plant Breeding and Biotechnology.2023; 11(3): 208.     CrossRef
• Gene-Based Allele Specific Marker for Resistance to Phytophthora sojae in Soybean (Glycine max L.)
  Young Eun Jang, Sungwoo Lee
  Plant Breeding and Biotechnology.2021; 9(2): 164.     CrossRef

The SUBMERGENCE 1 (SUB1) locus, conferring tolerance to complete inundation, was identified, and gel-based DNA markers, AEX1 and GnS2, were previously developed for marker-assisted breeding (MAB). However, a high throughput and high specific method, at low cost, is still required to detect Sub1 alleles. Kompetitive Allele Specific PCR (KASP) markers enable high throughput analysis for a large number of seeds, as well as detection of both alleles, in a single reaction. In this study, we developed KASP markers that can distinguish specific alleles at Sub1A loci based on single nucleotide polymorphisms (SNPs). Marker validations were carried out by genotyping of a segregating population with the developed KASP markers. The results from KASP assay and gel-based marker analysis were consistent for Sub1A alleles. KASP markers developed for Sub1A would be helpful due to high accuracy, low cost, and a high throughput genotyping feature in MAB.

Citations

Citations to this article as recorded by  

• Identification of KASP-SNP markers correlated with both growth and hypoxia tolerance traits in blunt snout bream (Megalobrama amblycephala)
  Yanluo Zhuo, Han Wang, Guanghai Dong, Huihu Wang, Guodong Zheng, Shuming Zou
  Aquaculture.2025; 608: 742745.     CrossRef
• Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1
  Md Ibrahim Khalil, Md Mahmudul Hassan, Swadesh Chandra Samanta, Abul Kashem Chowdhury, Md Zahid Hassan, Nasar Uddin Ahmed, Uzzal Somaddar, Sharmistha Ghosal, Arif Hasan Khan Robin, Ujjal Kumar Nath, Mohammad Golam Mostofa, David J. Burritt, Chien Van Ha,
  Plant Physiology and Biochemistry.2024; 206: 108224.     CrossRef
• KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance
  Bhawna Dipta, Salej Sood, Vikas Mangal, Vinay Bhardwaj, Ajay Kumar Thakur, Vinod Kumar, Brajesh Singh
  Molecular Biology Reports.2024;[Epub]     CrossRef
• Development of SNP Marker Set to Select Varieties Tolerant to Multiple Abiotic Stresses in Rice
  Jung-Woo Lee, Jung-Seok Oh, Soo-Cheul Yoo
  Plant Breeding and Biotechnology.2023; 11(3): 208.     CrossRef
• Development of Kompetitive Allele Specific PCR Markers for Anaerobic Germination 1 Locus in Rice
  Jung-Woo Lee, Joong Hyoun Chin, Soo-Cheul Yoo
  Plant Breeding and Biotechnology.2021; 9(1): 20.     CrossRef