Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea

Abstract

Sterility mosaic disease (SMD) is one of the serious production constraints that may lead to complete yield loss in pigeonpea. Three mapping populations including two recombinant inbred lines and one F₂, were used for phenotyping for SMD resistance at two locations in three different years. Genotyping-by-sequencing approach was used for simultaneous identification and genotyping of SNPs on above mentioned populations. In total, 212,464, 89,699 and 64,798 SNPs were identified in ICPL 20096 × ICPL 332 (PRIL_B), ICPL 20097 × ICP 8863 (PRIL_C) and ICP 8863 × ICPL 87119 (F₂) respectively. By using high-quality SNPs, genetic maps were developed for PRIL_B (1,101 SNPs; 921.21 cM), PRIL_C (484 SNPs; 798.25 cM) and F₂ (996 SNPs; 1,597.30 cM) populations. The average inter marker distance on these maps varied from 0.84 cM to 1.65 cM, which was lowest in all genetic mapping studies in pigeonpea. Composite interval mapping based QTL analysis identified a total of 10 QTLs including three major QTLs across the three populations. The phenotypic variance of the identified QTLs ranged from 3.6 to 34.3%. One candidate genomic region identified on CcLG11 seems to be promising QTL for molecular breeding in developing superior lines with enhanced resistance to SMD.

Figure 1

Frequency distribution of percent disease incidence (PDI) for Patancheru SMD isolate in various populations at different locations and years. The disease scoring was done on the basis of percentage of affected plants wherein 0% means complete resistance while 100% means complete susceptibility to SMD. The PDI was monitored for two consecutive years (2012–2013, 2013–2014) in ICPL 20096 × ICPL 332 (PRIL_B) and ICPL 20097 × ICP 8863 (PRIL_C) population while for one year (2015–2016) in ICP 8863 × ICPL 87119 (F₂) population. The PDI was divided into 10 categories and number of families falling in each category were plotted as bar plot. The PDI in ICPL 20096 × ICPL 332 (PRIL_B) population at Patancheru location and Rajendranagar, Hyderabad location is shown in a and b. Figure c and d represent PDI in ICPL 20097 × ICP 8863 (PRIL_C) population at Patancheru and Rajendranagar, Hyderabad location respectively, while, the Figure e represents the PDI in ICP 8863 × ICPL 87119 (F₂) population at Patancheru location.

Figure 2

Genome-wide distribution of SNPs identified in ICPL 20096 × ICPL 332 (PRIL_B), ICPL 20097 × ICP 8863 (PRIL_C) and ICP 8863 × ICPL 87119 (F₂) populations in pigeonpea. The number of SNPs identified within 100 Kb interval were calculated and plotted as a smooth line curve. The height of the curve is proportional to the number of SNPs within that 100 Kb interval. (A) Pigeonpea pseudomolecules, labelled as CcLG01 to CcLG11 and each pseudomolecule is shown in different colour. The numbers on arches represent the scale for the size of pseudomolecule in Mb. (B) Genome-wide distribution of SNPs identified in ICPL 20096 × ICPL 332 (PRIL_B) population (C) Genome-wide distribution of SNPs identified in ICPL 20097 × ICP 8863 (PRIL_C) population and (D) Genome-wide distribution of SNPs identified in ICP 8863 × ICPL 87119 (F₂) population in pigeonpea.

Figure 3

Genetic and QTL map comprising 1,101 SNPs and spanning 921.21 cM in ICPL 20096 × ICPL 332 (PRIL_B) population in pigeonpea. The scale on left side represents map distance in cM. The eleven linkage groups are shown as vertical bars and each horizontal line on the bar represent single SNP marker. Aggregation on horizontal lines indicate higher marker density on that particular linkage group. The single, consistent QTL (qSMD11.1) identified for SMD resistance on CcLG11 is shown by coloured rectangle.

Figure 4

Genetic and QTL map constructed using 484 SNPs and of 798.25 cM length in ICPL 20097 × ICP 8863 (PRIL_C) population in pigeonpea. The scale on left side represents map distance in cM. The eleven linkage groups are shown as vertical bars and each horizontal line on the bar represent single SNP marker. Aggregation on horizontal lines indicate higher marker density on that particular linkage group. Three and one rectangles on right side of CcLG02 and CcLG10 represent the four QTLs identified for SMD resistance in PRIL_C population.

Figure 5

Genetic and QTL map constructed using 996 SNPs and of 1,596.30 cM length in ICP 8863 × ICPL 87119 (F₂) population in pigeonpea. The scale on left side represents map distance in cM. The eleven linkage groups are shown as vertical bars and each horizontal line on the bar represent single SNP marker. Aggregation on horizontal lines indicate higher marker density on that particular linkage group. The QTLs identified for SMD resistance on various linkage groups have been shown as brown colored rectangle.