Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea.
In the present study, molecular mapping of high-resolution plant height QTLs was performed by integrating 3625 desi genome-derived GBS (genotyping-by-sequencing)-SNPs on an ultra-high resolution intra-specific chickpea genetic linkage map (dwarf/semi-dwarf desi cv. ICC12299 x tall kabuli cv. ICC8261). The identified six major genomic regions harboring six robust QTLs (11.5-21.3 PVE), associated with plant height, were mapped within <0.5 cM average marker intervals on six chromosomes. Five SNPs-containing genes tightly linked to the five plant height QTLs, were validated based upon their high potential for target trait association (12.9-20.8 PVE) in 65 desi and kabuli chickpea accessions. The vegetative tissue-specific expression, including higher differential up-regulation (>5-fold) of five genes especially in shoot, young leaf, shoot apical meristem of tall mapping parental accession (ICC8261) as compared to that of dwarf/semi-dwarf parent (ICC12299) was apparent. Overall, combining high-resolution QTL mapping with genetic association analysis and differential expression profiling, delineated natural allelic variants in five candidate genes (encoding cytochrome-c-biosynthesis protein, malic oxidoreductase, NADH dehydrogenase iron-sulfur protein, expressed protein and bZIP transcription factor) regulating plant height in chickpea. These molecular tags have potential to dissect complex plant height trait and accelerate marker-assisted genetic enhancement for developing cultivars with desirable plant height ideotypes in chickpea.
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
Alice
A
Kujur
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
Hari D
HD
Upadhyaya
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
Deepak
D
Bajaj
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
C L L
CL
Gowda
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
Shivali
S
Sharma
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
Akhilesh K
AK
Tyagi
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
Swarup K
SK
Parida
D000483:Alleles; D050976:Basic-Leucine Zipper Transcription Factors / Q000235:genetics; D002874:Chromosome Mapping; D029863:Cicer / Q000235:genetics / Q000254:growth & development* / Q000502:physiology; D020869:Gene Expression Profiling; D008040:Genetic Linkage / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D055106:Genome-Wide Association Study; D005838:Genotype; D007506:Iron-Sulfur Proteins / Q000235:genetics; D008291:Malate Dehydrogenase / Q000235:genetics; D018519:Meristem / Q000235:genetics*; D009245:NADH Dehydrogenase / Q000235:genetics; D018515:Plant Leaves / Q000235:genetics*; D018520:Plant Shoots / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*
D050976:Basic-Leucine Zipper Transcription Factors; D007506:Iron-Sulfur Proteins; D008291:Malate Dehydrogenase; D009245:NADH Dehydrogenase