Erratum to: Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection

In order to integrate genomics in breeding and development of drought-tolerant groundnut genotypes, identification of genomic regions/genetic markers for drought surrogate traits is essential. We used 3249 diversity array technology sequencing (DArTSeq) markers for a genetic analysis of 125 ICRISAT groundnut mini core collection evaluated in 2015 and 2017 for genome-wide marker-trait association for some physiological traits and to determine the magnitude of linkage disequilibrium (LD). Marker-trait association (MTA) analysis, probability values, and percent variation modelled by the markers were calculated using the GAPIT package via the KDCompute interface. The LD analysis showed that about 36% of loci pairs were in significant LD (p < 0.05 and r2 > 0.2) and 3.14% of the pairs were in complete LD. The MTAs studies revealed 20 significant MTAs (p < 0.001) with 11 markers. Four MTAs were identified for leaf area index, 13 for canopy temperature, one for chlorophyll content and two for normalized difference vegetation index. The markers explained 20.8% to 6.6% of the phenotypic variation observed. Most of the MTAs identified on the A subgenome were also identified on the respective homeologous chromosome on the B subgenome. This could be due to a common ancestor of the A and B genome which explains the linkage detected between markers lying on different chromosomes. The markers identified in this study can serve as useful genomic resources to initiate marker-assisted selection and trait introgression of groundnut for drought tolerance after further validation.

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Population Structure of the World Vegetable Center Mungbean Mini Core Collection and Genome-Wide Association Mapping of Loci Associated with Variation of Seed Coat Luster

Tropical Plant Biology ◽

10.1007/s12042-019-09236-0 ◽

2019 ◽

Vol 13 (1) ◽

pp. 1-12 ◽

Cited By ~ 6

Author(s):

Caleb Manamik Breria ◽

Ching Hsiang Hsieh ◽

Jo-Yi Yen ◽

Ramakrishnan Nair ◽

Chen-Yu Lin ◽

...

Keyword(s):

Population Structure ◽

Association Mapping ◽

Seed Coat ◽

Core Collection ◽

Genome Wide Association ◽

Mini Core Collection ◽

Genome Wide ◽

The World

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Association mapping of height and maturity across five environments using the sorghum mini core collection

Genome ◽

10.1139/g2012-034 ◽

2012 ◽

Vol 55 (6) ◽

pp. 471-479 ◽

Cited By ~ 25

Author(s):

Hari D. Upadhyaya ◽

Yi-Hong Wang ◽

Shivali Sharma ◽

Sube Singh

Keyword(s):

Association Mapping ◽

Core Collection ◽

Molecular Breeding ◽

Biomass Yield ◽

Biomass Productivity ◽

Energy Crop ◽

Mapping Technique ◽

Polymorphic Markers ◽

Mini Core Collection ◽

Simple Sequence

Sorghum is a potential energy crop thanks to its high biomass productivity and low input. Biomass yield in sorghum is defined by height and maturity. To develop molecular breeding tools for genetic improvement of these two traits, we have identified simple sequence repeat markers linked to height and maturity using a pool-based association mapping technique. The sorghum mini core collection was evaluated across five environments for height and maturity. Seven tall and seven short accessions were selected based on their height in all environments. Likewise, six early- and 10 late-maturing accessions were selected mostly based on their maturity in two post-rainy seasons. Two additional height pools were constructed based on phenotypes in one environment. The three pairs of pools were screened with 703 SSR markers and 39 polymorphic markers were confirmed by individual genotyping. Association mapping of the 39 markers with 242 accessions from the mini core collection identified five markers associated with maturity or height. All were clustered on chromosomes 6, 9, and 10 with previously mapped height and maturity markers or QTLs. One marker associated with both height and maturity was 84 kb from recently cloned Ma1. These markers will lay a foundation for identifying additional height and maturity genes in sorghum.

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Identification of four functional component content QTLs of brown rice in the Yunnan mini-core collection and its near-isogenic lines using association mapping

Cereal Research Communications ◽

10.1007/s42976-021-00191-9 ◽

2021 ◽

Author(s):

Xia Li ◽

Xiaomeng Yang ◽

Juan Du ◽

Zhiyuan Chen ◽

Mingliang Wei ◽

...

Keyword(s):

Association Mapping ◽

Core Collection ◽

Brown Rice ◽

Near Isogenic Lines ◽

Functional Component ◽

Isogenic Lines ◽

Mini Core Collection ◽

Component Content

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Association Mapping of Four Important Traits Using the USDA Rice Mini-Core Collection

Rice - Germplasm, Genetics and Improvement ◽

10.5772/56830 ◽

2014 ◽

Cited By ~ 1

Author(s):

Wengui Yan ◽

Aaron Jackson ◽

Melissa Jia ◽

Wei Zhou ◽

Haizheng Xiong ◽

...

Keyword(s):

Association Mapping ◽

Core Collection ◽

Mini Core Collection

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Genetic Variation And Association Mapping of Phenolic, Flavonoid Content And Antioxidant Capacity In USDA Rice Mini-Core Collection

10.21203/rs.3.rs-788391/v1 ◽

2021 ◽

Author(s):

Qingzhu Li ◽

Yongyi Ge ◽

Lily Yan Wang ◽

Kehu Li

Keyword(s):

Association Mapping ◽

Antioxidant Capacity ◽

Core Collection ◽

Phenolic Content ◽

Total Phenolics ◽

Genotypic Variation ◽

Genotypic Diversity ◽

Flavonoid Content ◽

Mini Core Collection ◽

Genome Wide

Abstract Genotypic diversity of total phenolics, flavonoid content and antioxidant capacity in the USDA rice mini-core collection was analyzed. Wide genotypic variation was found in total phenolics, flavonoid content and ABTS antioxidant capacity. Genome-wide association mapping between the three antioxidant traits and 155 SSR markers was conducted using Q + K model which takes both population structure (Q) and relative kinship (K) into consideration. A total of 23 marker trait association were identified with markers from Rc gene showed the strongest association with the three antioxidant traits. Rid12, RM484, RM162, RM5371 were commonly detected for phenolic content, flavonoids content and antioxidant capacity.

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Genetic variation and association mapping of phenolic, flavonoid content and antioxidant capacity in USDA rice mini-core collection

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01333-y ◽

2022 ◽

Author(s):

Kehu Li ◽

Qingzhu Li ◽

Lily Yan Wang ◽

Huanhuan Ren ◽

Yongyi Ge

Keyword(s):

Genetic Variation ◽

Association Mapping ◽

Antioxidant Capacity ◽

Core Collection ◽

Flavonoid Content ◽

Mini Core Collection

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Genome wide association analyses to understand genetic basis of flowering and plant height under three levels of nitrogen application in Brassica juncea (L.) Czern & Coss

Scientific Reports ◽

10.1038/s41598-021-83689-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Javed Akhatar ◽

Anna Goyal ◽

Navneet Kaur ◽

Chhaya Atri ◽

Meenakshi Mittal ◽

...

Keyword(s):

Plant Height ◽

Indian Subcontinent ◽

Association Studies ◽

Snp Markers ◽

Genome Wide Association ◽

Strong Interactions ◽

N Availability ◽

Oilseed Crop ◽

Genome Wide Association Studies ◽

Genome Wide

AbstractTimely transition to flowering, maturity and plant height are important for agronomic adaptation and productivity of Indian mustard (B. juncea), which is a major edible oilseed crop of low input ecologies in Indian subcontinent. Breeding manipulation for these traits is difficult because of the involvement of multiple interacting genetic and environmental factors. Here, we report a genetic analysis of these traits using a population comprising 92 diverse genotypes of mustard. These genotypes were evaluated under deficient (N75), normal (N100) or excess (N125) conditions of nitrogen (N) application. Lower N availability induced early flowering and maturity in most genotypes, while high N conditions delayed both. A genotyping-by-sequencing approach helped to identify 406,888 SNP markers and undertake genome wide association studies (GWAS). 282 significant marker-trait associations (MTA's) were identified. We detected strong interactions between GWAS loci and nitrogen levels. Though some trait associated SNPs were detected repeatedly across fertility gradients, majority were identified under deficient or normal levels of N applications. Annotation of the genomic region (s) within ± 50 kb of the peak SNPs facilitated prediction of 30 candidate genes belonging to light perception, circadian, floral meristem identity, flowering regulation, gibberellic acid pathways and plant development. These included over one copy each of AGL24, AP1, FVE, FRI, GID1A and GNC. FLC and CO were predicted on chromosomes A02 and B08 respectively. CDF1, CO, FLC, AGL24, GNC and FAF2 appeared to influence the variation for plant height. Our findings may help in improving phenotypic plasticity of mustard across fertility gradients through marker-assisted breeding strategies.

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