Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice

Abstract Grain size is a major determinant of grain yield in sorghum and other cereals. Over 100 quantitative trait loci (QTLs) of grain size have been identified in sorghum. However, no gene underlying any grain size QTL has been cloned. Here, we describe the fine mapping and cloning of one grain size QTL. From an F8 recombinant inbred line population derived from a cross between inbred lines 654 and LTR108, we identified 44 grain size QTLs. One QTL, qTGW1a, was detected consistently on the long arm of chromosome 1 in the span of 4 years. Using the extreme recombinants from an F2:3 fine-mapping population, qTGW1a was delimited within a ~33 kb region containing three predicted genes. One of them, SORBI_3001G341700, predicted to encode a G-protein γ subunit and homologous to GS3 in rice, is likely to be the causative gene for qTGW1a. qTGW1a appears to act as a negative regulator of grain size in sorghum. The functional allele of the putatively causative gene of qTGW1a from inbred line 654 decreased grain size, plant height, and grain yield in transgenic rice. Identification of the gene underlying qTGW1a advances our understanding of the regulatory mechanisms of grain size in sorghum and provides a target to manipulate grain size through genome editing.

Download Full-text

Selection and Fine Mapping of Chromosome-Specific cDNAs: Application to Human Chromosome 1

Genomics ◽

10.1006/geno.1996.0610 ◽

1996 ◽

Vol 38 (2) ◽

pp. 149-154 ◽

Cited By ~ 2

Author(s):

Mita Mancini ◽

Cinzia Sala ◽

Stefano Rivella ◽

Daniela Toniolo

Keyword(s):

Human Chromosome ◽

Fine Mapping ◽

Chromosome 1 ◽

Human Chromosome 1

Download Full-text

Fine mapping of RBG2, a quantitative trait locus for resistance to Burkholderia glumae, on rice chromosome 1

Molecular Breeding ◽

10.1007/s11032-015-0192-x ◽

2015 ◽

Vol 35 (1) ◽

Cited By ~ 7

Author(s):

Ritsuko Mizobuchi ◽

Hiroyuki Sato ◽

Shuichi Fukuoka ◽

Seiya Tsushima ◽

Masahiro Yano

Keyword(s):

Quantitative Trait Locus ◽

Fine Mapping ◽

Quantitative Trait ◽

Rice Chromosome ◽

Chromosome 1 ◽

Burkholderia Glumae ◽

Trait Locus

Download Full-text

Fine-mapping a locus for glucose tolerance using heterogeneous stock rats

Physiological Genomics ◽

10.1152/physiolgenomics.00178.2009 ◽

2010 ◽

Vol 41 (1) ◽

pp. 102-108 ◽

Cited By ~ 35

Author(s):

Leah C. Solberg Woods ◽

Katie Holl ◽

Michael Tschannen ◽

William Valdar

Keyword(s):

Glucose Tolerance ◽

Family Structure ◽

Fine Mapping ◽

Complex Traits ◽

Mixed Model ◽

Average Distance ◽

Tolerance Test ◽

Chromosome 1 ◽

Heterogeneous Stock ◽

Mixed Model Analysis

Heterogeneous stock (HS) animals provide the ability to map quantitative trait loci at high resolution [<5 Megabase (Mb)] in a relatively short time period. In the current study, we hypothesized that the HS rat colony would be useful for fine-mapping a region on rat chromosome 1 that has previously been implicated in glucose regulation. We administered a glucose tolerance test to 515 HS rats and genotyped these animals with 69 microsatellite markers, spaced an average distance of <1 Mb apart, on a 67 Mb region of rat chromosome 1. Using regression modeling of inferred haplotypes based on a hidden Markov model reconstruction and mixed model analysis in which we accounted for the complex family structure of the HS, we identified one sharp peak within this region. Using positional bootstrapping, we determined the most likely location of this locus is from 205.04 to 207.48 Mb. This work demonstrates the utility of HS rats for fine-mapping complex traits and emphasizes the importance of taking into account family structure when using highly recombinant populations.

Download Full-text

Confirmation and fine mapping of the chromosome 1 alcohol dependence risk locus

Molecular Psychiatry ◽

10.1038/sj.mp.4001429 ◽

2004 ◽

Vol 9 (3) ◽

pp. 312-319 ◽

Cited By ~ 17

Author(s):

J Lappalainen ◽

H R Kranzler ◽

I Petrakis ◽

L K Somberg ◽

G Page ◽

...

Keyword(s):

Alcohol Dependence ◽

Fine Mapping ◽

Chromosome 1 ◽

Risk Locus

Download Full-text

Mapping of QTLs Controlling Grain Shape and Populations Construction Derived from Related Residual Heterozygous Lines in Rice

Journal of Agricultural Science ◽

10.5539/jas.v8n9p104 ◽

2016 ◽

Vol 8 (9) ◽

pp. 104 ◽

Cited By ~ 2

Author(s):

Wenqiang Liu ◽

Xiaoxiang Li ◽

Kun Zhou ◽

Xiaowu Pan ◽

Yongchao Li ◽

...

Keyword(s):

Grain Size ◽

Quantitative Trait Locus ◽

Fine Mapping ◽

Grain Shape ◽

Width Ratio ◽

Phenotypic Variance ◽

Ril Population ◽

Trait Locus ◽

Grain Width ◽

Trait Correlation

Grain shape is usually characterized by grain length (GL), grain width (GW), grain thickness (GT) and length to width ratio (LWR), and controlled by quantitative trait locus (QTL). In this paper, QTL analysis was performed using an F2 population and an F8 recombinant inbred line (RIL) population from a cross Xiang743/Katy. A total of 38 QTLs for grain shape were detected and eight of them were repeatedly identified in both populations. Seven for GL, five for GW, five for GT, and eight for LWR were detected in F2 population, explaining totally phenotypic variance of 94.51%, 61.52%, 54.33% and 91.84%, respectively. Five for GL, three for GW, and five for LWR were detected in RILpopulation, explaining totally phenotypic variance of 39.83%, 37.52% and 36.71%, respectively. Many QTLs were located in similar intervals, contributing to complicated trait correlation. A few QTLs were mapped in intervals coincided with previously cloned genes associated with grain size. Two residual heterozygous lines (RHLs) were selected out on the basis of newly identified loci, populations derived from RHLs were constructed for fine mapping QTLs associated with grain shape.

Download Full-text

Effects on barley grain size, texture and modification during malting associated with three genes on chromosome 1

Journal of Cereal Science ◽

10.1016/0733-5210(95)90045-4 ◽

1995 ◽

Vol 22 (2) ◽

pp. 157-161 ◽

Cited By ~ 9

Author(s):

J.S Swanston

Keyword(s):

Grain Size ◽

Barley Grain ◽

Chromosome 1

Download Full-text

OsBRKq1, Related Grain Size Mapping, and Identification of Grain Shape Based on QTL Mapping in Rice

International Journal of Molecular Sciences ◽

10.3390/ijms22052289 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2289

Author(s):

Jae-Ryoung Park ◽

Dany Resolus ◽

Kyung-Min Kim

Keyword(s):

Grain Size ◽

Qtl Mapping ◽

Grain Weight ◽

Expression Level ◽

Chromosome 1 ◽

Gene Location ◽

World Population ◽

Genetic Traits ◽

Relative Expression ◽

Relative Expression Level

The world population is growing rapidly, and food shortage remains a critical issue. Quantitative trait locus (QTL) mapping is a statistical analytical method that uses both phenotypic and genotypic data. The purpose of QTL mapping is to determine the exact gene location for various complex traits. Increasing grain weight is a way to increase yield in rice. Genes related to grain size were mapped using the Samgang/Nagdong double haploid (SNDH) populations. Grain sizes were diversely distributed in SNDH 113 populations, and OsBRKq1 was detected on chromosome 1 in an analysis of QTL mapping that used 1000 grain weight, grain length, and grain width. OsBRKq1 exhibited high sequence similarity with the brassinosteroid leucine-rich repeat-receptor kinases of Arabidopsis thaliana and Zea mays. It was also predicted to have a similar function because of its high homology. OsBRKq1 interacts with various grain-size control genes. Among the SNDH populations, the analysis of the relative expression level during the panicle formation stage of OsBRKq1 in panicles of SNDH117, which has the largest grain size, and SNDH6, which has the smallest grain size, the relative expression level was significantly increased in SNDH117 panicles. SNDH populations have been advancing generations for 10 years; various genetic traits have been fixed and are currently being used as bridging parents. Therefore, the stable expression level of OsBRKq1 was confirmed via QTL mapping. In the future, OsBRKq1 can be effectively used to increase the yield of rice and solve food problems by increasing the size of seeds.

Download Full-text