Something Old and Something New: Wedding Recombinant Inbred Lines with Traditional Line Cross Analysis Increases Power to Describe Gene Interactions

Abstract Characterizing epistatic gene interactions is fundamental for understanding the genetic architecture of complex traits. However, due to the large number of potential gene combinations, detecting epistatic gene interactions is computationally demanding. A simple, easy-to-perform method for sensitive detection of epistasis is required. Due to their homozygous nature, use of recombinant inbred lines (RILs) excludes the dominance effect of alleles and interactions involving heterozygous genotypes, thereby allowing detection of epistasis in a simple and interpretable model. Here, we present an approach called RIL-StEp (recombinant inbred lines stepwise epistasis detection) to detect epistasis using single nucleotide polymorphisms in the genome. We applied the method to reveal epistasis affecting rice (Oryza sativa) seed hull color and leaf chlorophyll content and successfully identified pairs of genomic regions that presumably control these phenotypes. This method has the potential to improve our understanding of the genetic architecture of various traits of crops and other organisms.

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RIL-StEp: epistasis analysis of recombinant inbred lines (RILs) reveals candidate interacting genes that control rice seed hull color

10.1101/2020.06.09.141697 ◽

2020 ◽

Author(s):

Toshiyuki Sakai ◽

Akira Abe ◽

Motoki Shimizu ◽

Ryohei Terauchi

Keyword(s):

Recombinant Inbred ◽

Complex Traits ◽

Genetic Architecture ◽

Recombinant Inbred Lines ◽

Inbred Lines ◽

Gene Interactions ◽

Rice Seed ◽

Nucleotide Polymorphisms ◽

Control Seed ◽

Seed Hull

SummaryStudying epistatic gene interactions is important in understanding genetic architecture of complex traits in organisms. However, due to an enormous number of gene combinations to be analyzed, detection of epistatic gene-gene interactions has been computationally demanding. Here, we show a simple approach RIL-StEp, specialized to Recombinant Inbred Lines (RILs), to study epistasis using single nucleotide polymorphisms (SNPs) information of the genome. We applied the method to reveal epistasis affecting rice seed hull color phenotype, and successfully identified gene pairs that presumably control seed hull color. This method has a potential to enhancing our understanding of genetic architecture of various traits.

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Diverse sources of resistance to Spodoptera litura (F.) in groundnut

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.79s.1.8 ◽

2019 ◽

Vol 79 (01S) ◽

Author(s):

M. A. Saleem ◽

G. K. Naidu ◽

H. L. Nadaf ◽

P. S. Tippannavar

Keyword(s):

Recombinant Inbred ◽

Spodoptera Litura ◽

Hot Spot ◽

Recombinant Inbred Lines ◽

Insect Pest ◽

Inbred Lines ◽

Leaf Damage ◽

Botanical Variety ◽

Resistant Genotypes ◽

Botanical Varieties

Spodoptera litura an important insect pest of groundnut causes yield loss up to 71% in India. Though many effective chemicals are available to control Spodoptera, host plant resistance is the most desirable, economic and eco-friendly strategy. In the present study, groundnut mini core (184), recombinant inbred lines (318) and elite genotypes (44) were studied for their reaction to Spodoptera litura under hot spot location at Dharwad. Heritable component of variation existed for resistance to Spodoptera in groundnut mini core, recombinant inbred lines and elite genotypes indicating scope for selection of Spodoptera resistant genotypes. Only 29 (15%) genotypes belonging to hypogaea, fastigiata and hirsuta botanical varieties under mini core set, 15 transgressive segregants belonging to fastigiata botanical variety among 318 recombinant inbred lines and three genotypes belonging to hypogaea and fastigiata botanical varieties under elite genotypes showed resistance to Spodoptera litura with less than 10% leaf damage. Negative correlation existed between resistance to Spodoptera and days to 50 per cent flowering indicating late maturing nature of resistant genotypes. Eight resistant genotypes (ICG 862, ICG 928, ICG 76, ICG 2777, ICG 5016, ICG 12276, ICG 4412 and ICG 9905) under hypogaea botanical variety also had significantly higher pod yield. These diverse genotypes could serve as potential donors for incorporation of Spodoptera resistance in groundnut.

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