Genetic analysis for rice grain quality traits in the YVB stable variant line using RAD-seq.
The future of rice breeding will likely be built on the basis of the further utilization of heterosis between elite cultivars and genetic resources from distant subspecies of rice. Previous studies have proved that exogenous genomic DNA transformation methods can be used to transfer genetic information from distant relatives (donor) into cultivated rice (recipient). However, the mechanism underlying this form of genetic transfer is poorly characterized, and the genes that cause the phenotypic changes in these variants are typically difficult to identify. This study examined YVB, a stable variant line with greatly improved grain quality traits that was derived from an indica variety (V20B) by transferring genomic DNA of O.minuta through the "spike-stalk injection method (SIM)". We used restriction-site associated DNA sequencing technology (RAD-seq) to evaluate a population of BC1F5 backcross lines (YVB × V20B); the RAD-seq data were used to construct a genetic linkage map with high-density SNPs for use in association analysis exploring genotype-phenotype relationships at the whole-genome level. A total of 17 quantitative trait loci (QTLs) for rice quality traits were mapped to chromosomes 3, 5, 6, 8, and 9. 8 major QTLs controlling different phenotypic variations were mapped to the same region of chromosome 5. This region contained the GS5 gene for grain weight and the qSW5/GW5 gene for grain width. This study provides new resources and insights into the molecular mechanisms of grain trait phenotypic variation and the transmission of genetic information via the introduction of genomic DNA to a distantly related crop relative species.
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 736 Yuanda Erlu, Changsha, 410125, China. py225666@163.com.
Yan
Y
Peng
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 736 Yuanda Erlu, Changsha, 410125, China. huyuanyi237@163.com.
Yuanyi
Y
Hu
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 736 Yuanda Erlu, Changsha, 410125, China.
Bigang
B
Mao
Key Lab of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China.
Haitao
H
Xiang
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 736 Yuanda Erlu, Changsha, 410125, China.
Ye
Y
Shao
Longping Branch, Graduate School of Central South University, Changsha, 410125, China.
Yinlin
Y
Pan
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 736 Yuanda Erlu, Changsha, 410125, China.
Xiabing
X
Sheng
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 736 Yuanda Erlu, Changsha, 410125, China.
Yaokui
Y
Li
Key Lab of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China.
Xuemei
X
Ni
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 736 Yuanda Erlu, Changsha, 410125, China.
Yumei
Y
Xia
Key Lab of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China.
Gengyun
G
Zhang
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 736 Yuanda Erlu, Changsha, 410125, China.
Longping
L
Yuan
Key Lab of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China. quanzhiwu@genomics.cn.
Zhiwu
Z
Quan
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, 736 Yuanda Erlu, Changsha, 410125, China. brzhaohhrrcrice@163.com.
Bingran
B
Zhao
D001947:Breeding / Q000379:methods; D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant / Q000235:genetics; D002523:Edible Grain / Q000235:genetics*; D005820:Genetic Testing / Q000379:methods; D005838:Genotype; D007178:Inbreeding / Q000379:methods; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
Genomic DNA transformation; QTL mapping; RAD-seq; Rice quality traits; Wild rice