KASP mapping of QTLs for yield components using a RIL population in Basmati rice (Oryza sativa L.)

Ashfaq, Hamza; Rani, Reena; Perveen, Nusrat; Babar, Allah Ditta; Maqsood, Umer; Asif, Muhammad; Steele, Katherine A.; Arif, Muhammad

doi:10.1007/s10681-023-03206-0

Cited by 4 publications

References 54 publications

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Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa)

Steele,

Quinton-Tulloch,

Vyas

et al. 2024

G3: Genes, Genomes, Genetics

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This study aimed to broaden applicability of KASP for Oryza sativa across diverse genotypes through incorporation of ambiguous (degenerate) bases into their primer designs and to validate 4000 of them for genotyping applications. A bioinformatics pipeline was used to compare 129 rice genomes from 89 countries with the indica reference genome R498 and generate ∼1.6 million KASP designs for the more common variants between R498 and the other genomes. Of the designs, 98,238 were for predicted functional markers. Up to five KASP each for 1024 breeder-selected loci were assayed in a panel of 178 diverse rice varieties, generating 3366 validated KASP. The 84% success rate was within the normal range for KASP demonstrating that the ambiguous bases do not compromise efficacy. The 3366-trait-specific marker panel was applied for population structure analysis in the diversity panel and resolved them into four expected groups. Target variations in thirteen of the genome sequences used for designs were compared with the corresponding KASP genotypes of other accessions of the same thirteen varieties in the diversity panel. There was agreement across 12 varieties for 79% of markers. Ten varieties had high agreement (>88%) but a variety selected from a landrace had only 46.5% agreement. Breeders can now search for the validated KASP and >1 million so-far untested designs across three alternative reference genomes (including Niponbare MSU7), search for designs proximal to previously published SSR markers and retrieve the target variations in 129 rice genomes plus their genomic locations with +/-25 bp flanking sequences.

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Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa)

Steele,

Quinton-Tulloch,

Vyas

et al. 2024

G3: Genes, Genomes, Genetics

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Allele Mining and Development of Kompetitive Allele Specific PCR (KASP) Marker in Plant Breeding

Sharma,

Kumar,

Bhadana

2023

Recent Trends in Plant Breeding and Genetic Improvement

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Crop improvement refers to the systematic approach of discovering and selecting plants that possess advantageous alleles for specific target genes. The foundation of crop improvement initiatives typically relies on the fundamental concepts of genetic diversity and the genetic architecture of agricultural plants. Allele mining is a contemporary and efficacious technique utilized for the identification of naturally occurring allelic variations within genes that exhibit advantageous characteristics. Consequently, the utilization of allele mining has significant potential as a feasible approach for enhancing crop-related endeavors. The gene pool of a plant exhibits a substantial degree of genetic variety, characterized by the presence of a multitude of mechanism genes. The utilization of genetic variants for the detection and separation of novel alleles of genes that display favorable traits from the current gene pool, and their subsequent incorporation into the development of improved cultivars through the application of marker-assisted selection, is of utmost importance.

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QTL Analysis for Yield-Related Traits Using the Recombinant Inbred Lines Derived From a Cross Between ‘Chamdongjin’ and ‘Younghojinmi’

Park,

Seo,

Park

et al. 2024

Korean J. Breed. Sci.

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Chamdongjin' is a near-isogenic line with enhanced disease resistance compared to 'Sindongjin,' a mega-cultivar in Korea. 'Younghojinmi' is the rice cultivar with the highest taste quality among the premium cultivars. This study conducted quantitative trait loci (QTL) analysis on yield-related traits using the recombinant inbred lines derived from a cross between 'Chamdongjin' and 'Younghojinmi' to elucidate genetic interaction. We utilized KASP markers and a target-capture sequencing SNP genotyping platform to address the insufficient genetic diversity of the population using Korean japonica cultivars. A QTL associated with heading date (HD), qHd8, was detected, and the candidate gene Hd18 was identified. The hd18 allele delayed HD by 3 days and reduced the brown/rough rice ratio (BRR) by 0.3%. QTLs associated with culm length (CL), panicle length (PL), and yield (g/plant), namely qCL1, qPL1_2023, and qYield1_2023, respectively, were detected, and the candidate gene SD1 was identified. The sd1 allele shortened CL and PL by 11 and 0.8 cm, respectively, and reduced the yield by 2.3 g. It also reduced the number of spikelets per panicle (NS) by 10 and decreased the ratio of ripened grains (RRG) by 2.6 %. QTLs associated with 1,000-grain weight (TGW), NS, and BRR, namely qTGW3, qNS3, and qBRR3_ 2023, respectively, were detected, and the candidate gene GS3 was identified. The gs3 allele increased TGW and BRR by 3.8 g and 0.4%, respectively, and reduced NS by 12. It also reduced RRG content by 1.9% and increased the yield by 1.7 g. The QTL associated with the number of panicles per hill (PN), qTN3, and the candidate gene, OsTB1, were identified. The OsTB1 TGTG allele reduced PN by 1.3 and affected the increase in NS and RRG by 10 and 1.4%, respectively. The allele combinations of SD1, GS3, and OsTB1 were analyzed to assess their effects on yield-related traits. NS and RRG were influenced by trait variations, depending on the combination background of other alleles during allele substitution. 'Jeonju 697,' an elite breeding line exhibiting improved lodging resistance with shortened CL, was selected by substituting SD1 with sd1 while maintaining the Hd18-gs3-OsTB1 TGTG allele combination of 'Chamdongjin.' This is expected to be a practical alternative for addressing the lodging problem in 'Chamdongjin.'

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KASP mapping of QTLs for yield components using a RIL population in Basmati rice (Oryza sativa L.)

Cited by 4 publications

References 54 publications

Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa)

Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa)

Allele Mining and Development of Kompetitive Allele Specific PCR (KASP) Marker in Plant Breeding

QTL Analysis for Yield-Related Traits Using the Recombinant Inbred Lines Derived From a Cross Between ‘Chamdongjin’ and ‘Younghojinmi’

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