QTL-seq and linkage analysis identified KASP marker linked to non-parchment trait in edible podded pea
The nonparchment layer trait in edible podded pea inhibits the formation of sclerenchymatous tissue in the pod wall which makes the pods edible in nature In the present study genetics and genomic regions controlling nonparchment layer trait was studied in edible podded pea Inheritance study from cross Honey Snap X Punjab89 showed that it was governed by single major recessive gene along with certain modifiers Putative genomic regions associated with the nonparchment layer were identified using BSA seq approach where two extreme phenotypic pools were constructed by identifying extreme plants for the given trait Downstream analysis through QTLseqr identified one major genomic region of 60 Mb located at 592 to 652 Mb on chromosome 5 and was designated as qNpp51 Within this region 26 KASP markers were developed and out of which 11 showed polymorphism in two parents and two bulks The phenotypic and genotypic data from 257 F3 population was used to construct linkage map using QTL IciMapping that narrowed down the qNpp51 region to 12 Mb flanked by Psp618703255 and Psp606633411 KASP markers on Chr05 The QTL qNpp51 was identified at LOD 19 and explained 28 percent of the total phenotypic variation showing 064 and 008 of additive and dominant effects respectively The closely linked KASP marker Psp618703255 was able to predict 8085 per cent of plants accurately in a diverse panel of P sativum var hortense P sativum var macrocarpon P sativum var saccharatum and BC1F2 population derived from cross Punjab89 X Honey Snap X Punjab89 Moreover using EXPASY tool it showed nonsynonym substitution in the exonic region of putative candidate exocyst complex component EXO70H1 gene These findings can be used for marker assisted selection to accelerate the non parchment layer breeding programs in edible podded pea
The nonparchment layer trait in edible podded pea inhibits the formation of sclerenchymatous tissue in the pod wall which makes the pods edible in nature In the present study genetics and genomic regions controlling nonparchment layer trait was studied in edible podded pea Inheritance study from cross Honey Snap X Punjab89 showed that it was governed by single major recessive gene along with certain modifiers Putative genomic regions associated with the nonparchment layer were identified using BSA seq approach where two extreme phenotypic pools were constructed by identifying extreme plants for the given trait Downstream analysis through QTLseqr identified one major genomic region of 60 Mb located at 592 to 652 Mb on chromosome 5 and was designated as qNpp51 Within this region 26 KASP markers were developed and out of which 11 showed polymorphism in two parents and two bulks The phenotypic and genotypic data from 257 F3 population was used to construct linkage map using QTL IciMapping that narrowed down the qNpp51 region to 12 Mb flanked by Psp618703255 and Psp606633411 KASP markers on Chr05 The QTL qNpp51 was identified at LOD 19 and explained 28 percent of the total phenotypic variation showing 064 and 008 of additive and dominant effects respectively The closely linked KASP marker Psp618703255 was able to predict 8085 per cent of plants accurately in a diverse panel of P sativum var hortense P sativum var macrocarpon P sativum var saccharatum and BC1F2 population derived from cross Punjab89 X Honey Snap X Punjab89 Moreover using EXPASY tool it showed nonsynonym substitution in the exonic region of putative candidate exocyst complex component EXO70H1 gene These findings can be used for marker assisted selection to accelerate the non parchment layer breeding programs in edible podded pea
Indian Biological Data Centre