Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L. esculentum genetic background: A tool for gene mapping and gene discovery

Genome ◽  
2000 ◽  
Vol 43 (5) ◽  
pp. 803-813 ◽  
Author(s):  
Antonio J Monforte ◽  
Steve D Tanksley
Keyword(s):  
Genetic Resources ◽  
Recombinant Inbred ◽  
Genetic Background ◽  
Recombinant Inbred Lines ◽  
Pollen Viability ◽  
Inbred Lines ◽  
Allelic Frequency ◽  
Isogenic Line ◽  
Genomic Regions ◽  
Backcross Recombinant Inbred Lines

A novel population consisted of a set of 99 near isogenic lines (NILs) and backcross recombinant inbred lines (BCRILs) derived from a cross between the cultivated tomato Lycopersicon esculentum cv. E6206 and L. hirsutum accession LA1777 is presented. Most of the lines contain a single defined introgression from L. hirsutum in the L. esculentum genetic background and together, the lines provide a coverage of more than the 85% of the L. hirsutum genome. These lines represent a new tool to uncover the genetic resources hidden in L. hirsutum as well as to study the genes responsible of its unique biology. Furthermore, the study of the allelic frequency and heterozygosity among BCRILs showed that specific genomic regions were likely subjected to unintentional selection pressures during the stock development. Genes involved in the reproductive behavior and (or) pollen viability are hypothesized to be responsible for these alterations.Key words: germplasm, near isogenic line, tomato, genetic resources.

scholarly journals Genome Sequence and QTL Analyses Using Backcross Recombinant Inbred Lines (BILs) and BILF1 Lines Uncover Multiple Heterosis-related Loci

2020 ◽  
Vol 21 (3) ◽  
pp. 780 ◽  
Author(s):  
Yahui Yu ◽  
Mengmeng Zhu ◽  
Yue Cui ◽  
Yu Liu ◽  
Zhenyu Li ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Genome Sequence ◽  
Recombinant Inbred ◽  
Genetic Background ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Japonica Rice ◽  
Grain Number ◽  
Grain Number Per Panicle ◽  
Backcross Recombinant Inbred Lines

Heterosis is an interesting topic for both breeders and biologists due to its practical importance and scientific significance. Cultivated rice (Oryza sativa L.) consists of two subspecies, indica and japonica, and hybrid rice is the predominant form of indica rice in China. However, the molecular mechanism underlying heterosis in japonica remains unclear. The present study determined the genome sequence and conducted quantitative trait locus (QTL) analysis using backcross recombinant inbred lines (BILs) and BILF1 lines to uncover the heterosis-related loci for rice yield increase under a japonica genetic background. The BIL population was derived from an admixture variety Habataki and japonica variety Sasanishiki cross to improve the genetic diversity but maintain the genetic background close to japonica. The results showed that heterosis in F1 mainly involved grain number per panicle. The BILF1s showed an increase in grain number per panicle but a decrease in plant height compared with the BILs. Genetic analysis then identified eight QTLs for heterosis in the BILF1s; four QTLs were detected exclusively in the BILF1 population only, presenting a mode of dominance or super-dominance in the heterozygotes. An additional four loci overlapped with QTLs detected in the BIL population, and we found that Grains Height Date 7 (Ghd7) was correlated in days to heading in both BILs and BILF1s. The admixture genetic background of Habataki was also determined by subspecies-specific single nucleotide polymorphisms (SNPs). This investigation highlights the importance of high-throughput sequencing to elucidate the molecular mechanism of heterosis and provides useful germplasms for the application of heterosis in japonica rice production.

scholarly journals Molecular mapping of QTLs for resistance to early and late Fusarium wilt in chickpea

2014 ◽  
Vol 50 (No. 2) ◽  
pp. 171-176 ◽  
Author(s):  
B.S. Patil ◽  
R.L. Ravikumar ◽  
J.S. Bhat ◽  
C.D. Soregaon
Keyword(s):  
Fusarium Wilt ◽  
Recombinant Inbred ◽  
Molecular Mapping ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Reference Map ◽  
Genomic Regions ◽  
Marker Distance

A molecular map of chickpea was constructed using F<sub>9</sub>:F<sub>10</sub> recombinant inbred lines from an intraspecific cross between Fusarium wilt susceptible (JG 62) and resistant (WR 315) genotypes. A total of 23 markers with LOD scores of &gt; 3.0 were mapped on the recombinant inbred lines (RILs). Twenty sequence tagged microsatellites (STMSs) and three amplified fragment length polymorphisms (AFLPs) covered 300.2 cM in five linkage groups at an average inter-marker distance of 13 cM. Early and late wilting due to Fusarium infection was recorded in RILs at 30&nbsp;and 60 DAS, respectively. There was a significant variation among RILs for wilt resistance for both early and late wilting. QTLs associated with early (30 days after sowing (DAS)) and late (60&nbsp;DAS) wilting are located on LG II. The flanking markers for these QTLs were the same as those of previous reports. Five STMS markers located on LG II of reference map (interspecific) were mapped on LG II of the present map (intraspecific) with minor changes in the order of markers indicating the conservation of these genomic regions across the Cicer species.

scholarly journals QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativa L.)

2012 ◽  
Vol 12 (1) ◽  
pp. 137 ◽  
Author(s):  
Balram Marathi ◽  
Smriti Guleria ◽  
Trilochan Mohapatra ◽  
Rajender Parsad ◽  
Nagarajan Mariappan ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Qtl Analysis ◽  
Recombinant Inbred ◽  
Oryza Sativa L ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Plant Type ◽  
Genomic Regions

scholarly journals Signatures of Dobzhansky-Muller Incompatibilities in the Genomes of Recombinant Inbred Lines

2015 ◽  
Author(s):  
Maria Colomé-Tatché ◽  
Frank Johannes
Keyword(s):  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Develop Model ◽  
Selection Signatures ◽  
In The Wild ◽  
Lower Fertility ◽  
Viable Seeds ◽  
Genomic Regions ◽  
Theoretical Results

In the construction of Recombinant Inbred Lines (RILs) from two divergent inbred parents certain genotype (or epigenotype) combinations may be functionally "incompatible" when brought together in the genomes of the progeny, thus resulting in sterility or lower fertility. Natural selection against these epistatic combinations during inbreeding can change haplotype frequencies and distort linkage disequilibrium (LD) relations between loci within and across chromosomes. These LD distortions have received increased experimental attention, because they point to genomic regions that may drive Dobzhansky-Muller-type of reproductive isolation and, ultimately, speciation in the wild. Here we study the selection signatures of two-locus epistatic incompatibility models and quantify their impact on the genetic composition of the genomes of 2-way RILs obtained by selfing. We also consider the biases introduced by breeders when trying to counteract the loss of lines by selectively propagating only viable seeds. Building on our theoretical results, we develop model-based maximum likelihood (ML) tests which can be employed in pairwise genome scans for incompatibility loci using multi-locus genotype data. We illustrate this ML approach in the context of two published A. thaliana RIL panels. Our work lays the theoretical foundation for studying more complex systems such as RILs obtained by sibling mating and/or from multi-parental crosses.

scholarly journals Identification of stably expressed QTL for heading date using reciprocal introgression line and recombinant inbred line populations in rice

2012 ◽  
Vol 94 (5) ◽  
pp. 245-253
Author(s):  
LI-RUI CHENG ◽  
JUN-MIN WANG ◽  
GUOYOU YE ◽  
CHENG-GANG LUO ◽  
JIAN-LONG XU ◽  
...  
Keyword(s):  
Recombinant Inbred ◽  
Genetic Background ◽  
Recombinant Inbred Lines ◽  
Heading Date ◽  
Introgression Line ◽  
Hainan Island ◽  
Inbred Lines ◽  
Genetic Background Effect ◽  
Different Populations ◽  
Degree Of Similarity

SummaryTwo sets of reciprocal introgression lines (ILs) and a population of recombinant inbred lines (RILs) derived from the cross between japonica cultivar Xiushui09 and indica breeding line IR2061-520-6-9 (abbreviated as IR2061) were used to identify QTL for heading date (HD). Phenotyping was conducted in Hainan Island for two winter seasons (2007 and 2009). Nine QTLs were detected in the ILs with Xiushui09 background (XS-ILs), and four of which were repeatedly mapped across 2 years. Five QTLs were identified in the ILs with IR2061 background (IR-ILs), and three of which were commonly detected in 2 years. All commonly detected QTL had the same direction of gene effect. Seven QTL for HD were identified in the RILs in 2009. Only three (25%) QTLs were commonly detected using all the three populations (XS-ILs, IR-ILs and RILs). The number of commonly identified QTLs among populations was related to degree of similarity of their genetic backgrounds, suggesting that the genetic background effect is important for detecting HD QTL. QHd7 and QHd10b stably expressed in different populations and across years thus would be exploited in rice breeding programme. Moreover, lines with both of QHd7 and QHd10b resulted in at least 3 days earlier than lines with only one of them QTL, showing evident pyramiding effect.

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