Whole‐genome resequencing and transcriptome analysis provide insights on aphid‐resistant quantitative trait loci/genes in Sorghum bicolor

Abstract

The sorghum aphid (Melanaphis sacchari) has emerged as a serious pest for Sorghum bicolor and a major factor limiting its production worldwide. In this study, whole‐genome resequencing of resistant and susceptible bulks from a recombinant inbred line (RIL) population was conducted together with transcriptome analysis of the parent to identify genes underlying aphid resistance. In the NGS‐based bulked segregation analysis (BSA), using a total of 920,389 genome‐wide high‐confidence markers, four QTLs, qtlMs‐6.1, qtlMs‐6.2, qtlMs‐6.3, and qtlMs‐6.4, were identified on chromosome 6. Based on comparative transcriptome analysis, 245 differentially expressed genes (DEGs,190 upregulated and 55 downregulated) and 576 DEGs (336 upregulated and 240 downregulated) were identified at 4 dpi in 407B (resistant) and 7B (susceptible), respectively. The DEGs in 407B were enriched in ‘DNA replication’, ‘flavone and flavonol biosynthesis’ and ‘flavonoid biosynthesis’, which are associated with plant stress resistance. The QTL‐seq study identified a SNP marker (Chr6: 2686447C>G) that was validated on a diverse panel and could be used in molecular marker‐assisted selection to improve aphid resistance in sorghum.

Genome-Wide Association Mapping of Resistance to the Sugarcane Aphid in Sorghum bicolor

“…Some studies have attempted to understand the molecular basis of this interaction in sorghum as monogenic, though it is believed to be oligogenic and polygenic [23][24][25]56 . Most of the studies highlighted the importance of RMES1 locus located on SBI-06 and the causative variants around this region to be the major resistance gene for sugarcane aphid resistance in sorghum depending on the source of resistance used in these studies 24,25,27,56 . SCA resistance is monogenic (single locus) for RME6 ACK60 x RTx2783.…”

“…Among aphid resistance traits, the maximum number of markers,16, was identi ed on SBI-06. Recent studies have speci cally dissected regions around the RMES1 locus and found several NBS-LRR containing genes that were associated with resistance gene products 25,27,56 . In our investigation, we were able to locate LRR motifs and Avr9 elicitor response protein within 200 kb region for markers associated with aphid damage and aphid count on SBI-06.…”

“…In a recent study, the combination of whole-genome resequencing and transcriptome analysis showed that differential gene expressions (DEGs) from the resistant source were enriched in 'DNA replication' and ' avonoid biosynthesis' 27 . In our study, two avonoid biosynthesis genes (Sobic.005G033801 and Sobic.007G059200) were identi ed within 200 kb of S5_3230535 and S7_6208175 markers on SBI-05 and SBI-07.…”

“…There were four markers, namely, S1_5101469, S2_61431704, S6_58686833, and S6_60922873, that were signi cantly associated with NDRE and found in either case with or without using owering time as a covariate and the rest 16 SNPs were new loci when owering time was not used as covariate. Some of the important notable ones were S6_32034639 marker was found ~366 kb of the sugarcane aphid resistance QTL, qtlMs-6.2, located between 31,020,371 to 32,400,770 bp 27 . Among several loci identi ed, SNP S8_59192389 associated with NDRE is approximately10 kb away from the calmodulin, (CAM) gene, Sobic.008G159100 (SBI-08: 59203243 to 59204321), a differentially expressed gene family observed by Kiani & Szczepaniec 45 .…”

“…Knoll and Cuevas 26 identi ed the same RMES1 region from a SC112-14 (resistant) x PI 609251 (susceptible) recombinant inbred line (RIL) population. Zhang et al 27 identi ed four QTLs for sugarcane aphid resistance on SBI-06 from resistant source 407B. One of these QTLs, qtlMs-6.1, overlaps with the RMES1 locus.…”