Development of Wide-Compatible Indica Lines by Pyramiding Multiple Neutral Alleles of Indica–Japonica Hybrid Sterility Loci

Guo, Jie; Li, Yun; Xiong, Liang; Yan, Tao; Zou, Jinsong; Dai, Ziju; Tang, Guang; Sun, Kangli; L, Xin; Yang, Weifeng; Tan, Qi; Zhu, Haitao; Zeng, Ruizhen; Wang, Shaokui; Zhang, Guiquan

doi:10.3389/fpls.2022.890568

Cited by 7 publications

(6 citation statements)

References 38 publications

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“…These suggested that the accessions carrying a few NFAs provide potential targets for the BCAA biofortified rice breeding programs via the loci pyramiding strategy. It was successfully applied in the improvement of various agronomic traits, such as plant height, grain number, hybrid sterility, and disease resistance [ 57 , 58 , 59 , 60 , 61 ]. In the present study, higher BCAA levels were mostly shown in the japonica accessions than in the indica accessions ( Figure 1 A–C), suggesting that the japonica rice has the potential of the increase in the BACC content in indica rice through the direct hybridization with elite varieties.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains

Sui,

Che,

Zhong

et al. 2023

Plants

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Rice (Oryza sativa L.) is a globally important food source providing carbohydrates, amino acids, and dietary fiber for humans and livestock. The branched-chain amino acid (BCAA) level is a complex trait related to the nutrient quality of rice. However, the genetic mechanism underlying the BCAA (valine, leucine, and isoleucine) accumulation in rice grains remains largely unclear. In this study, the grain BCAA contents and 239,055 SNPs of a diverse panel containing 422 rice accessions were adopted to perform a genome-wide association study (GWAS) using a recently proposed 3VmrMLM model. A total of 357 BCAA-content-associated main-effect quantitative trait nucleotides (QTNs) were identified from 15 datasets (12 BCAA content datasets and 3 BLUP datasets of BCAA). Furthermore, the allelic variation of two novel candidate genes, LOC_Os01g52530 and LOC_Os06g15420, responsible for the isoleucine (Ile) content alteration were identified. To reveal the genetic basis of the potential interactions between the gene and environmental factor, 53 QTN-by-environment interactions (QEIs) were detected using the 3VmrMLM model. The LOC_Os03g24460, LOC_Os01g55590, and LOC_Os12g31820 were considered as the candidate genes potentially contributing to the valine (Val), leucine (Leu), and isoleucine (Ile) accumulations, respectively. Additionally, 10 QTN-by-QTN interactions (QQIs) were detected using the 3VmrMLM model, which were putative gene-by-gene interactions related to the Leu and Ile contents. Taken together, these findings suggest that the implementation of the 3VmrMLM model in a GWAS may provide new insights into the deeper understanding of BCAA accumulation in rice grains. The identified QTNs/QEIs/QQIs serve as potential targets for the genetic improvement of rice with high BCAA levels.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains

Sui,

Che,

Zhong

et al. 2023

Plants

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“…According to the well-known theory put forth by Ikehashi and Araki (1986), F1 sterility was mostly brought on by embryo sac abortion, which was determined by the genotype of S 5 located in chromosome 6, and indica was S 5 i S 5 i in genotype as well as japonica S 5 j S 5 j (Yang et al, 2009;Zhang et al, 2020;Seo et al, 2020;Kallugudi et al, 2022) hence The S 5 locus on chromosome 6 became the primary genetic cause of embryo sac sterility due to several allelic interactions (Lee et al, 2021;Ouyang et al, 2022). Nevertheless, hybrid fertility was decreased as a result of interactions between the indica and japonica alleles at each of the loci (Xie et al, 2019;Guo et al, 2022;Kallugudi et al, 2022). Yang further explained that because to gene interactions, the indica and japonica parent types' S5iS5j hybrids were also infertile S 5 i and S 5 j .…”

Section: Introductionmentioning

confidence: 99%

“…When crossed to indica or japonica subspecies, WCVs can overcome obstacles to reproduction and result in fertile hybrids. Hybrids between indica and japonica parent lines that carry the S 5 n (wide-compatible gene) would have high or normal fertility regardless of whether they have the S 5 nS 5 i or S 5 nS 5 j genotype Ghaleb et al, 2020;Guo et al, 2022). Wide-compatibility varieties (WCVs) allowed the reproductive barrier between the indica and japonica subspecies to be breached and gave rice breeding programs the opportunity to create inter-sub specific hybrids.…”

Section: Introductionmentioning

confidence: 99%

Sequencing of S5 gene in autotetraploid rice japonica and indica to overcome F1 hybrids embryo sac sterility

Fimanekeni,

Nabieu,

Xiang-Dong

2023

Int. J. Genet. Mol. Biol.

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Autotetraploid rice is a new germplasm developed through diploid chromosome doubling. Hybrids developed by indica autotetraploid rice crossed by japonica autotetraploid rice has clear biological advantage on F 1 , causing widespread concerns for special research evolution to evaluate and utilize F 1 hybrid vigor. However, the widespread fertility of F 1 indica and japonica autotetraploid rice is low, which makes it difficult to direct utilization of F 1 vigor. In diploid indica and japonica rice, the fertility of F 1 hybrids is also proved to be low. Embryo sac infertility is known to be one of the most important reasons for hybrid sterility and many studies has indicated that the primary cause of F1 sterility was abortion of the embryo sac, which was identified by the genotype of the S5 gene on the chromosome. Previous studies have cloned S 5 based on common wild rice and cultivated rice and S 5 sequence was obtained and studied. In this paper, typical sequence of different materials of S 5 japonica and indica rice group of autotetraploid hybrids observed with whole-mount eosin B-staining confocal laser scanning microscopy WE-CLSM was utilized, to overcome F 1 hybrids embryo sac sterility.

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“…The HJX74-SSSLs were widely used to detect QTLs for traits of agronomic importance (Zhang et al, 2012 ; Zhu et al, 2014 , 2018 ; Yang et al, 2016 , 2021a , b ; Zhou et al, 2017b ; Pan et al, 2021 ; Zhan et al, 2021 ; Fu et al, 2022 ), to clone genes of functional importance, and to mine alleles of functional variants (Zeng et al, 2006 ; Teng et al, 2012 ; Wang et al, 2012 ; Fang et al, 2019 ; Sui et al, 2019 ; Gao et al, 2021 ; Zhan et al, 2022 ). Using the HJX74-SSSL library as a platform for rice design, a series of cytoplasmic male sterility (CMS), maintainer and restorer lines, and wide-compatible indica lines (WCILs) were developed (Dai et al, 2015 , 2016 ; Luan et al, 2019 ; Guo et al, 2022 ). Recently, the SSSLs were used to detect QTLs controlling SER in rice.…”

Section: Introductionmentioning

confidence: 99%

Reconstruction of the High Stigma Exsertion Rate Trait in Rice by Pyramiding Multiple QTLs

Tan

Chen

et al. 2022

Front. Plant Sci.

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Asian cultivated rice is a self-pollinating crop, which has already lost some traits of natural outcrossing in the process of domestication. However, male sterility lines (MSLs) need to have a strong outcrossing ability to produce hybrid seeds by outcrossing with restorer lines of male parents in hybrid rice seed production. Stigma exsertion rate (SER) is a trait related to outcrossing ability. Reconstruction of the high-SER trait is essential in the MSL breeding of rice. In previous studies, we detected eighteen quantitative trait loci (QTLs) for SER from Oryza sativa, Oryza glaberrima, and Oryza glumaepatula using single-segment substitution lines (SSSLs) in the genetic background of Huajingxian 74 (HJX74). In this study, eleven of the QTLs were used to develop pyramiding lines. A total of 29 pyramiding lines with 2–6 QTLs were developed from 10 SSSLs carrying QTLs for SER in the HJX74 genetic background. The results showed that the SER increased with increasing QTLs in the pyramiding lines. The SER in the lines with 5–6 QTLs was as high as wild rice with strong outcrossing ability. The epistasis of additive by additive interaction between QTLs in the pyramiding lines was less-than-additive or negative effect. One QTL, qSER3a-sat, showed minor-effect epistasis and increased higher SER than other QTLs in pyramiding lines. The detection of epistasis of QTLs on SER uncovered the genetic architecture of SER, which provides a basis for using these QTLs to improve SER levels in MSL breeding. The reconstruction of the high-SER trait will help to develop the MSLs with strong outcrossing ability in rice.

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Development of Wide-Compatible Indica Lines by Pyramiding Multiple Neutral Alleles of Indica–Japonica Hybrid Sterility Loci

Cited by 7 publications

References 38 publications

Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains

Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains

Sequencing of S5 gene in autotetraploid rice japonica and indica to overcome F1 hybrids embryo sac sterility

Reconstruction of the High Stigma Exsertion Rate Trait in Rice by Pyramiding Multiple QTLs

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