Mapping of QTL for agronomic traits using high-density SNPs with an RIL population in maize

Jin, Kyu; Choi, Ik‐Young; Park, Jong Yeol; Choi, Jae‐Keun; Ryu, Si‐Hwan; Lee, Ju Kyong

doi:10.1007/s13258-021-01169-x

Cited by 9 publications

(9 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Among these MTAs, 8 MTAs were unknown, and 32 SNP and SSR marker associations with 26 genes were detected in the Bin 9.02~9.03 region, which corresponds to a physical position between 20,346,749 to 100,030,452 base pairs (bps). Moreover, in our previous studies [ 43 , 44 ] for QTL mapping, we detected two QTL regions between umc1634 and wx1 using SSR and SNP markers and between PZE-109022525 and PZE-109024175 using SNP markers. The 14 statistically significant markers at 9 genes (GRMZM2G147319, GRMZM2G024993, GRMZM2G121333, GRMZM2G396553, GRMZM2G118355, GRMZM2G118687, GRMZM2G118690, GRMZM2G082855, GRMZM2G370155) in the Q + K MLM and PCA + K MLM were detected between previous QTL intervals ( Table 2 and Table 3 ).…”

Section: Discussionmentioning

confidence: 99%

“…A population of 80 F 7:8 RILs used in this study was constructed by single-seed descent between normal maize inbred line Mo17 (United States Corn Belt) and waxy maize inbred line KW7 (Korean waxy maize landrace) at the Maize Experiment Station, Gangwon Agricultural Research and Extension Service, Hongcheon [ 43 , 51 ]. Analysis of amylose content was performed on both parental lines as well as on the 80 RILs in kernel, and this study used three replicates for each line and an average value [ 44 ].…”

Section: Methodsmentioning

confidence: 99%

“…A total of 14,968 SSR and SNP genotypes for RILs were generated in this study from two different studies for genetic and QTL mapping [ 43 , 44 ]. Among them, the 546 informative markers (541 SSRs and 5 SNPs) reported in a previous study by Sa et al (2015) [ 43 ] were obtained after filtering by a chi-square test ( p < 0.05) [ 43 ], and the 14,422 SNP markers reported in a previous study by Sa et al (2021) [ 44 ] were obtained for association mapping after filtering of the Illumina MaizeSNP50 Bead-Chip (Illumina, Inc. San Diego, CA, USA) of 56,110 maize SNPs, which covers 19,540 genes developed from the B73 reference sequence [ 44 , 52 ]. Among the 56,110 SNPs, many SNPs were removed, such as unanchored SNPs; missing, heterozygote, and monomorphic markers in parental lines; over 10% missing in the RIL population; and SNPs on duplicated positions.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers

Jin

Park

Jang

et al. 2023

Plants

Self Cite

View full text Add to dashboard Cite

The ratio of amylose to amylopectin in maize kernel starch is important for the appearance, structure, and quality of food products and processing. This study aimed to identify quantitative trait loci (QTLs) controlling amylose content in maize through association mapping with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. The average value of amylose content for an 80-recombinant-inbred-line (RIL) population was 8.8 ± 0.7%, ranging from 2.1 to 15.9%. We used two different analyses—Q + K and PCA + K mixed linear models (MLMs)—and found 38 (35 SNP and 3 SSR) and 32 (29 SNP and 3 SSR) marker–trait associations (MTAs) associated with amylose content. A total of 34 (31 SNP and 3 SSR) and 28 (25 SNP and 3 SSR) MTAs were confirmed in the Q + K and PCA + K MLMs, respectively. This study detected some candidate genes for amylose content, such as GRMZM2G118690-encoding BBR/BPC transcription factor, which is used for the control of seed development and is associated with the amylose content of rice. GRMZM5G830776-encoding SNARE-interacting protein (KEULE) and the uncharacterized marker PUT-163a-18172151-1376 were significant with higher R2 value in two difference methods. GRMZM2G092296 were also significantly associated with amylose content in this study. This study focused on amylose content using a RIL population derived from dent and waxy inbred lines using molecular markers. Future studies would be of benefit for investigating the physical linkage between starch synthesis genes using SNP and SSR markers, which would help to build a more detailed genetic map and provide new insights into gene regulation of agriculturally important traits.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers

Jin

Park

Jang

et al. 2023

Plants

Self Cite

View full text Add to dashboard Cite

show abstract

“…Traditionally, QTL mapping studies have been performed with linkage mapping strategies using segregating populations derived from biparental crosses, such as F 2 populations, recombinant inbred lines (RILs), double-haploid populations (DHs), and single-segment substitution lines (SSSLs) [20][21][22][23]. Genome-wide association studies (GWASs) benefit from abundant diversity, enabling the locations of identified QTLs to be inferred with a high resolution; however, the inherent population structure and presence of rare variants in natural populations reduce GWAS statistical power [19].…”

Section: Introductionmentioning

confidence: 99%

Identification of two new QTLs of maize (Zea mays L.) underlying kernel row number using the HNAU-NAM1 population

et al. 2022

View full text Add to dashboard Cite

Background Maize kernel row number (KRN) is one of the most important yield traits and has changed greatly during maize domestication and selection. Elucidating the genetic basis of KRN will be helpful to improve grain yield in maize. Results Here, we measured KRN in four environments using a nested association mapping (NAM) population named HNAU-NAM1 with 1,617 recombinant inbred lines (RILs) that were derived from 12 maize inbred lines with a common parent, GEMS41. Then, five consensus quantitative trait loci (QTLs) distributing on four chromosomes were identified in at least three environments along with the best linear unbiased prediction (BLUP) values by the joint linkage mapping (JLM) method. These QTLs were further validated by the separate linkage mapping (SLM) and genome-wide association study (GWAS) methods. Three KRN genes cloned through the QTL assay were found in three of the five consensus QTLs, including qKRN1.1, qKRN2.1 and qKRN4.1. Two new QTLs of KRN, qKRN4.2 and qKRN9.1, were also identified. On the basis of public RNA-seq and genome annotation data, five genes highly expressed in ear tissue were considered candidate genes contributing to KRN. Conclusions This study carried out a comprehensive analysis of the genetic architecture of KRN by using a new NAM population under multiple environments. The present results provide solid information for understanding the genetic components underlying KRN and candidate genes in qKRN4.2 and qKRN9.1. Single-nucleotide polymorphisms (SNPs) closely linked to qKRN4.2 and qKRN9.1 could be used to improve inbred yield during molecular breeding in maize.

show abstract

“…Plant growth related traits such as biomass (FW) and height are controlled by quantitative trait loci (QTLs) (Bac‐Molenaar et al, 2015). To map those agronomically important QTLs, high‐density genetic maps have been constructed for crops such as maize (Sa et al, 2021), sorghum (Kajiya‐Kanegae et al, 2020), rice (Zhu et al, 2018), wheat (Miki et al, 2020), soybean (Wang et al, 2020) and pea (Barilli et al, 2018). Kajiya‐Kanegae et al (2020) used a recombinant inbred line (RIL) population of NOG and BTx623 to construct a high‐density genetic map in sorghum with restriction site‐associated DNA sequencing (RAD‐seq), and 13 QTLs were detected on Chromosomes 2, 3, 6, 7, 8 and 9, of which five QTLs were for days to heading, three for PH and total fresh shoot weight and two for Brix.…”

Section: Introductionmentioning

confidence: 99%

Construction of high density genetic map and quantitative trait locus mapping in a sorghum Tx623A × sudangrass S722 population

Wang

Jin

et al. 2022

Grassland Science

View full text Add to dashboard Cite

Sorghum-sudanense is a hybrid of sorghum and Sudanese grass and is widely used in animal husbandry and aquaculture because of its high yield, excellent quality and wide adaptability. Using high-throughput sequencing, we constructed a high-density genetic map of sorghum Tx623A Â sudangrass S722 with 103 recombinant inbred lines (RILs) in this study and mapped quantitative trait loci (QTLs) for plant height (PH), stem diameter (SD), tiller number (TN), fresh weight (FW) and dry weight per plant (DW). The map included 1610 markers with a total length of 2329 cM and QTL mapping identified 19 QTLs, including two for PH, three for SD, four for TN, four for FW and five for DW. We detected two QTL clusters containing overlapping QTLs for PH, FW and DW. Orthologs of three SD candidate genes from maize were found within two SD QTLs. The identification of these QTLs will be useful for cloning the corresponding genes for these traits and developing marker-assisted selection (MAS) in future sorghum breeding programs.

show abstract

Mapping of QTL for agronomic traits using high-density SNPs with an RIL population in maize

Cited by 9 publications

References 60 publications

Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers

Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers

Identification of two new QTLs of maize (Zea mays L.) underlying kernel row number using the HNAU-NAM1 population

Construction of high density genetic map and quantitative trait locus mapping in a sorghum Tx623A × sudangrass S722 population

Contact Info

Product

Resources

About