TY  - JOUR
AU  - Kumar, Sandeep
AU  - Saini, Dinesh Kumar
AU  - Jan, Farkhandah
AU  - Jan, Sofora
AU  - Tahir, Mohd
AU  - Đalović, Ivica
AU  - Latković, Dragana
AU  - Khan, Mohd Anwar
AU  - Kuma, Sundeep
AU  - Vikas, V. K.
AU  - Kumar, Upendra
AU  - Kumar, Sundip
AU  - Dhaka, Narendra Singh
AU  - Dhankher, Om Parkash
AU  - Rustgi, Sachin
AU  - Mir, Reyazul Rouf
PY  - 2023
UR  - http://fiver.ifvcns.rs/handle/123456789/3562
AB  - Yellow or stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici (Pst) is an important disease of wheat that threatens wheat production. Since developing resistant cultivars offers a viable solution for disease management, it is essential to understand the genetic basis of stripe rust resistance. In recent years, meta-QTL analysis of identified QTLs has gained popularity as a way to dissect the genetic architecture underpinning quantitative traits, including disease resistance. Systematic meta-QTL analysis involving 505 QTLs from 101 linkage-based interval mapping studies was conducted for stripe rust resistance in wheat. For this purpose, publicly available high-quality genetic maps were used to create a consensus linkage map involving 138,574 markers. This map was used to project the QTLs and conduct meta-QTL analysis. A total of 67 important meta-QTLs (MQTLs) were identified which were refined to 29 high-confidence MQTLs. The confidence interval (CI) of MQTLs ranged from 0 to 11.68 cM with a mean of 1.97 cM. The mean physical CI of MQTLs was 24.01 Mb, ranging from 0.0749 to 216.23 Mb per MQTL. As many as 44 MQTLs colocalized with marker–trait associations or SNP peaks associated with stripe rust resistance in wheat. Some MQTLs also included the following major genes- Yr5, Yr7, Yr16, Yr26, Yr30, Yr43, Yr44, Yr64, YrCH52, and YrH52. Candidate gene mining in high-confidence MQTLs identified 1,562 gene models. Examining these gene models for differential expressions yielded 123 differentially expressed genes, including the 59 most promising CGs. We also studied how these genes were expressed in wheat tissues at different phases of development
PB  - Springer Nature
T2  - BMC Genomics
T1  - Comprehensive meta-QTL analysis for dissecting the genetic architecture of stripe rust resistance in bread wheat
SP  - 259
VL  - 24
DO  - 10.1186/s12864-023-09336-y
ER  - 

@article{
author = "Kumar, Sandeep and Saini, Dinesh Kumar and Jan, Farkhandah and Jan, Sofora and Tahir, Mohd and Đalović, Ivica and Latković, Dragana and Khan, Mohd Anwar and Kuma, Sundeep and Vikas, V. K. and Kumar, Upendra and Kumar, Sundip and Dhaka, Narendra Singh and Dhankher, Om Parkash and Rustgi, Sachin and Mir, Reyazul Rouf",
year = "2023",
abstract = "Yellow or stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici (Pst) is an important disease of wheat that threatens wheat production. Since developing resistant cultivars offers a viable solution for disease management, it is essential to understand the genetic basis of stripe rust resistance. In recent years, meta-QTL analysis of identified QTLs has gained popularity as a way to dissect the genetic architecture underpinning quantitative traits, including disease resistance. Systematic meta-QTL analysis involving 505 QTLs from 101 linkage-based interval mapping studies was conducted for stripe rust resistance in wheat. For this purpose, publicly available high-quality genetic maps were used to create a consensus linkage map involving 138,574 markers. This map was used to project the QTLs and conduct meta-QTL analysis. A total of 67 important meta-QTLs (MQTLs) were identified which were refined to 29 high-confidence MQTLs. The confidence interval (CI) of MQTLs ranged from 0 to 11.68 cM with a mean of 1.97 cM. The mean physical CI of MQTLs was 24.01 Mb, ranging from 0.0749 to 216.23 Mb per MQTL. As many as 44 MQTLs colocalized with marker–trait associations or SNP peaks associated with stripe rust resistance in wheat. Some MQTLs also included the following major genes- Yr5, Yr7, Yr16, Yr26, Yr30, Yr43, Yr44, Yr64, YrCH52, and YrH52. Candidate gene mining in high-confidence MQTLs identified 1,562 gene models. Examining these gene models for differential expressions yielded 123 differentially expressed genes, including the 59 most promising CGs. We also studied how these genes were expressed in wheat tissues at different phases of development",
publisher = "Springer Nature",
journal = "BMC Genomics",
title = "Comprehensive meta-QTL analysis for dissecting the genetic architecture of stripe rust resistance in bread wheat",
pages = "259",
volume = "24",
doi = "10.1186/s12864-023-09336-y"
}

Kumar, S., Saini, D. K., Jan, F., Jan, S., Tahir, M., Đalović, I., Latković, D., Khan, M. A., Kuma, S., Vikas, V. K., Kumar, U., Kumar, S., Dhaka, N. S., Dhankher, O. P., Rustgi, S.,& Mir, R. R.. (2023). Comprehensive meta-QTL analysis for dissecting the genetic architecture of stripe rust resistance in bread wheat. in BMC Genomics
Springer Nature., 24, 259.
https://doi.org/10.1186/s12864-023-09336-y

Kumar S, Saini DK, Jan F, Jan S, Tahir M, Đalović I, Latković D, Khan MA, Kuma S, Vikas VK, Kumar U, Kumar S, Dhaka NS, Dhankher OP, Rustgi S, Mir RR. Comprehensive meta-QTL analysis for dissecting the genetic architecture of stripe rust resistance in bread wheat. in BMC Genomics. 2023;24:259.
doi:10.1186/s12864-023-09336-y .

Kumar, Sandeep, Saini, Dinesh Kumar, Jan, Farkhandah, Jan, Sofora, Tahir, Mohd, Đalović, Ivica, Latković, Dragana, Khan, Mohd Anwar, Kuma, Sundeep, Vikas, V. K., Kumar, Upendra, Kumar, Sundip, Dhaka, Narendra Singh, Dhankher, Om Parkash, Rustgi, Sachin, Mir, Reyazul Rouf, "Comprehensive meta-QTL analysis for dissecting the genetic architecture of stripe rust resistance in bread wheat" in BMC Genomics, 24 (2023):259,
https://doi.org/10.1186/s12864-023-09336-y . .

TY  - JOUR
AU  - Kumar, Vivek
AU  - Sharma, Hemant
AU  - Saini, Lalita
AU  - Tyagi, Archasvi
AU  - Jain, Pooja
AU  - Singh, Yogita
AU  - Balyan, Priyanka
AU  - Kumar, Sachin
AU  - Jan, Sofora
AU  - Mir, Reyazul Rouf
AU  - Đalović, Ivica
AU  - Singh, Krishna Pal
AU  - Kumar, Upendra
AU  - Malik, Vijai
PY  - 2022
UR  - http://fiver.ifvcns.rs/handle/123456789/3203
AB  - The core particle represents the catalytic portions of the 26S proteasomal complex. The genes encoding a- and b-subunits play a crucial role in protecting plants against various environmental stresses by controlling the quality of newly produced proteins. The 20S proteasome gene family has already been reported in model plants such as Arabidopsis and rice; however, they have not been studied in oilseed crops such as rapeseed (Brassica napus L.). In the present study, we identified 20S proteasome genes for a- (PA) and b-subunits (PB) in B. napus through systematically performed gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 82 genes, comprising 35 BnPA and 47 BnPB of the 20S proteasome, were revealed in the B. napus genome. These genes were distributed on all 20 chromosomes of B. napus and most of these genes were duplicated on homoeologous chromosomes. The BnPA (a1-7) and BnPB (b1-7) genes were phylogenetically placed into seven clades. The pattern of expression of all the BnPA and BnPB genes was also studied using RNA-seq datasets under biotic and abiotic stress conditions. Out of 82 BnPA/PB genes, three exhibited high expression under abiotic stresses, whereas two genes were overexpressed in response to biotic stresses at both the seedling and flowering stages. Moreover, an additional eighteen genes were expressed under normal conditions. Overall, the current findings developed our understanding of the organization of the 20S proteasome genes in B. napus and provided specific BnPA/PB genes for further functional research in response to abiotic and biotic stresses.
PB  - Frontiers Media S.A.
T2  - Frontiers in Plant Science
T1  - Phylogenomic analysis of 20S proteasome gene family reveals stress-responsive patterns in rapeseed (Brassica napus L.)
SP  - 1037206
VL  - 13
DO  - 10.3389/fpls.2022.1037206
ER  - 

@article{
author = "Kumar, Vivek and Sharma, Hemant and Saini, Lalita and Tyagi, Archasvi and Jain, Pooja and Singh, Yogita and Balyan, Priyanka and Kumar, Sachin and Jan, Sofora and Mir, Reyazul Rouf and Đalović, Ivica and Singh, Krishna Pal and Kumar, Upendra and Malik, Vijai",
year = "2022",
abstract = "The core particle represents the catalytic portions of the 26S proteasomal complex. The genes encoding a- and b-subunits play a crucial role in protecting plants against various environmental stresses by controlling the quality of newly produced proteins. The 20S proteasome gene family has already been reported in model plants such as Arabidopsis and rice; however, they have not been studied in oilseed crops such as rapeseed (Brassica napus L.). In the present study, we identified 20S proteasome genes for a- (PA) and b-subunits (PB) in B. napus through systematically performed gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 82 genes, comprising 35 BnPA and 47 BnPB of the 20S proteasome, were revealed in the B. napus genome. These genes were distributed on all 20 chromosomes of B. napus and most of these genes were duplicated on homoeologous chromosomes. The BnPA (a1-7) and BnPB (b1-7) genes were phylogenetically placed into seven clades. The pattern of expression of all the BnPA and BnPB genes was also studied using RNA-seq datasets under biotic and abiotic stress conditions. Out of 82 BnPA/PB genes, three exhibited high expression under abiotic stresses, whereas two genes were overexpressed in response to biotic stresses at both the seedling and flowering stages. Moreover, an additional eighteen genes were expressed under normal conditions. Overall, the current findings developed our understanding of the organization of the 20S proteasome genes in B. napus and provided specific BnPA/PB genes for further functional research in response to abiotic and biotic stresses.",
publisher = "Frontiers Media S.A.",
journal = "Frontiers in Plant Science",
title = "Phylogenomic analysis of 20S proteasome gene family reveals stress-responsive patterns in rapeseed (Brassica napus L.)",
pages = "1037206",
volume = "13",
doi = "10.3389/fpls.2022.1037206"
}

Kumar, V., Sharma, H., Saini, L., Tyagi, A., Jain, P., Singh, Y., Balyan, P., Kumar, S., Jan, S., Mir, R. R., Đalović, I., Singh, K. P., Kumar, U.,& Malik, V.. (2022). Phylogenomic analysis of 20S proteasome gene family reveals stress-responsive patterns in rapeseed (Brassica napus L.). in Frontiers in Plant Science
Frontiers Media S.A.., 13, 1037206.
https://doi.org/10.3389/fpls.2022.1037206

Kumar V, Sharma H, Saini L, Tyagi A, Jain P, Singh Y, Balyan P, Kumar S, Jan S, Mir RR, Đalović I, Singh KP, Kumar U, Malik V. Phylogenomic analysis of 20S proteasome gene family reveals stress-responsive patterns in rapeseed (Brassica napus L.). in Frontiers in Plant Science. 2022;13:1037206.
doi:10.3389/fpls.2022.1037206 .

Kumar, Vivek, Sharma, Hemant, Saini, Lalita, Tyagi, Archasvi, Jain, Pooja, Singh, Yogita, Balyan, Priyanka, Kumar, Sachin, Jan, Sofora, Mir, Reyazul Rouf, Đalović, Ivica, Singh, Krishna Pal, Kumar, Upendra, Malik, Vijai, "Phylogenomic analysis of 20S proteasome gene family reveals stress-responsive patterns in rapeseed (Brassica napus L.)" in Frontiers in Plant Science, 13 (2022):1037206,
https://doi.org/10.3389/fpls.2022.1037206 . .