Dataset Information

Bulked segregant analysis reveals candidate genes responsible for dwarf formation in woody oilseed crop castor bean.

ABSTRACT: Plant dwarfism is a desirable agronomic trait in non-timber trees, but little is known about the physiological and molecular mechanism underlying dwarfism in woody plants. Castor bean (Ricinus communis) is a typical woody oilseed crop. We performed cytological observations within xylem, phloem and cambia tissues, revealing that divergent cell growth in all tissues might play a role in the dwarf phenotype in cultivated castor bean. Based on bulked segregant analyses for a F₂ population generated from the crossing of a tall and a dwarf accession, we identified two QTLs associated with plant height, covering 325 candidate genes. One of these, Rc5NG4-1 encoding a putative IAA transport protein localized in the tonoplast was functionally characterized. A non-synonymous SNP (altering the amino acid sequence from Y to C at position 218) differentiated the tall and dwarf plants and we confirmed, through heterologous yeast transformation, that the IAA uptake capacities of Rc5NG4-1Y and Rc5NG4-1C were significantly different. This study provides insights into the physiological and molecular mechanisms of dwarfing in woody non-timber economically important plants, with potential to aid in the genetic breeding of castor bean and other related crops.

SUBMITTER: Wang Z

PROVIDER: S-EPMC7973431 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Bulked segregant analysis reveals candidate genes responsible for dwarf formation in woody oilseed crop castor bean.

Wang Zaiqing Z Yu Anmin A Li Fei F Xu Wei W Han Bing B Cheng Xiaomao X Liu Aizhong A

Scientific reports 20210318 1

Plant dwarfism is a desirable agronomic trait in non-timber trees, but little is known about the physiological and molecular mechanism underlying dwarfism in woody plants. Castor bean (Ricinus communis) is a typical woody oilseed crop. We performed cytological observations within xylem, phloem and cambia tissues, revealing that divergent cell growth in all tissues might play a role in the dwarf phenotype in cultivated castor bean. Based on bulked segregant analyses for a F<sub>2</sub> population ...[more]

PMID: 33737619

Similar Datasets

Project description:BackgroundCommon bean was one of the first crops that benefited from the development and utilization of molecular marker-assisted selection (MAS) for major disease resistance genes. Efficiency of MAS for breeding common bean is still hampered, however, due to the dominance, linkage phase, and loose linkage of previously developed markers. Here we applied in silico bulked segregant analysis (BSA) to the BeanCAP diversity panel, composed of over 500 lines and genotyped with the BARCBEAN_3 6K SNP BeadChip, to develop codominant and tightly linked markers to the I gene controlling resistance to Bean common mosaic virus (BCMV).ResultsWe physically mapped the genomic region underlying the I gene. This locus, in the distal arm of chromosome Pv02, contains seven putative NBS-LRR-type disease resistance genes. Two contrasting bulks, containing BCMV host differentials and ten BeanCAP lines with known disease reaction to BCMV, were subjected to in silico BSA for targeting the I gene and flanking sequences. Two distinct haplotypes, containing a cluster of six single nucleotide polymorphisms (SNP), were associated with resistance or susceptibility to BCMV. One-hundred and twenty-two lines, including 115 of the BeanCAP panel, were screened for BCMV resistance in the greenhouse, and all of the resistant or susceptible plants displayed distinct SNP haplotypes as those found in the two bulks. The resistant/susceptible haplotypes were validated in 98 recombinant inbred lines segregating for BCMV resistance. The closest SNP (~25-32 kb) to the distal NBS-LRR gene model for the I gene locus was targeted for conversion to codominant KASP (Kompetitive Allele Specific PCR) and CAPS (Cleaved Amplified Polymorphic Sequence) markers. Both marker systems accurately predicted the disease reaction to BCMV conferred by the I gene in all screened lines of this study.ConclusionsWe demonstrated the utility of the in silico BSA approach using genetically diverse germplasm, genotyped with a high-density SNP chip array, to discover SNP variation at a specific targeted genomic region. In common bean, many disease resistance genes are mapped and their physical genomic position can now be determined, thus the application of this approach will facilitate further development of codominant and tightly linked markers for use in MAS.

Project description:Waterlogging has increasingly become one of the major constraints to maize productivity in some maize production zones because it causes serious yield loss. Bulked segregant RNA-seq (BSR-seq) has been widely applied to profile candidate genes and map associated Single Nucleotide Polymorphism (SNP) markers in many species. In this study, 10 waterlogging sensitive and eight tolerant inbred lines were selected from 60 maize inbred lines with waterlogging response determined and preselected by the International Maize and Wheat Improvement Center (CIMMYT) from over 400 tropical maize inbred lines. BSR-seq was performed to identify differentially expressed genes and SNPs associated with waterlogging tolerance. Upon waterlogging stress, 354 and 1094 genes were differentially expressed in the tolerant and sensitive pools, respectively, compared to untreated controls. When tolerant and sensitive pools were compared, 593 genes were differentially expressed under untreated and 431 genes under waterlogged conditions, of which 122 genes overlapped. To validate the BSR-seq results, the expression levels of six genes were determined by qRT-PCR. The qRT-PCR results were consistent with BSR-seq results. Comparison of allelic polymorphism in mRNA sequences between tolerant and sensitive pools revealed 165 (normal condition) and 128 (waterlogged condition) high-probability SNPs. We found 18 overlapping SNPs with genomic positions mapped. Eighteen SNPs were contained in 18 genes, and eight and nine of 18 genes were responsive to waterlogging stress in tolerant and sensitive lines, respectively. Six alleles of the 18 originated from tolerant pool were significantly up-regulated under waterlogging, but not those from sensitive pool. Importantly, one allele (GRMZM2G055704) of the six genes was mapped between umc1619 and umc1948 on chromosome 1 where a QTL associated with waterlogging tolerance was identified in a previous research, strongly indicating that GRMZM2G055704 is a candidate gene responsive to waterlogging. Our research contributes to the knowledge of the molecular mechanism for waterlogging tolerance in maize.

Dataset Information

Bulked segregant analysis reveals candidate genes responsible for dwarf formation in woody oilseed crop castor bean.

Publications

Bulked segregant analysis reveals candidate genes responsible for dwarf formation in woody oilseed crop castor bean.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets