Allelic variations of the Wx locus in cultivated rice and their use in the development of hybrid rice in China

In rice endosperms, the Waxy (Wx) gene is important for amylose synthesis, and various Wx alleles control the amylose content and affect the taste of cooked rice. Herein, we report the cloning of the ancestral allele Wxlv of the Wx locus, which affects the mouthfeel of rice grains by modulating the size of amylose molecules. Using evolutionary analysis, we demonstrated that Wxlv originated directly from wild rice, and the three major Wx alleles in cultivated rice (Wxb, Wxa, and Wxin) differentiated after the substitution of one base pair at the functional sites. These data indicate that the Wxlv allele played an important role in artificial selection and domestication. The findings also shed light on the evolution of various Wx alleles, which have greatly contributed to improving the eating and cooking quality of rice.

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Improving cooking and eating quality of Xieyou57, an elite indica hybrid rice, by marker-assisted selection of the Wx locus

Euphytica ◽

10.1007/s10681-011-0377-2 ◽

2011 ◽

Vol 179 (2) ◽

pp. 355-362 ◽

Cited By ~ 18

Author(s):

Dahu Ni ◽

Shilu Zhang ◽

Sheng Chen ◽

Yong Xu ◽

Li Li ◽

...

Keyword(s):

Marker Assisted Selection ◽

Hybrid Rice ◽

Eating Quality ◽

Wx Locus ◽

Cooking And Eating Quality ◽

Indica Hybrid Rice ◽

Selection Of

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Exploring Natural Allelic Variations of the β-Triketone Herbicide Resistance Gene HIS1 for Application in indica Rice and Particularly in Two-Line Hybrid Rice

Rice ◽

10.1186/s12284-020-00448-7 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Qiming Lv ◽

Xiuli Zhang ◽

Dingyang Yuan ◽

Zhiyuan Huang ◽

Rui Peng ◽

...

Keyword(s):

Resistance Gene ◽

Seed Production ◽

High Efficiency ◽

Hybrid Rice ◽

Indica Rice ◽

Rice Paddy ◽

Rice Seed ◽

Rice Varieties ◽

Allelic Variations ◽

Fertility Restorers

Abstract Background Benzobicyclon (BBC) is a β-triketone herbicide (bTH) used in rice paddy fields. It has the advantages of high efficiency, low toxicity, high crop safety, and good environmental compatibility, and shows efficacy against paddy weeds resistant to other types of herbicides. However, as some important indica rice varieties are susceptible to BBC, BBC is currently only registered and applied in japonica rice cultivation areas. Results By analyzing haplotypes of the bTHs broad-spectrum resistance gene HIS1 and phenotypes for BBC in 493 major indica rice accessions in China, we identified a novel non-functional allelic variant of HIS1 in addition to the previously reported 28-bp deletion. Through detection with markers specific to the two non-functional mutations, it was clear that 25.4% of indica conventional varieties, 59.9% of fertility restorers, and 15.9% of sterile lines were susceptible to BBC. In addition, due to natural allelic variations of the HIS1 gene in the sterile and restorer lines, some two-line hybrid sterile lines were sensitive to bTHs, and the corresponding restorers were resistant. We showed the potential effectiveness of using bTHs to address the issue of two-line hybrid rice seed purity stemming from the self-crossing of sterile lines during hybrid rice seed production. Finally, allelic variations of the HIS1 gene may also play an important role in the mechanized seed production of hybrid rice. Conclusions Our findings offer guidance for the application of BBC in indica rice areas and provide a non-transgenic approach to address the seed purity issue of two-line hybrid rice.

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Exploring natural allelic variations of the β-triketone herbicide resistance gene HIS1 for application in indica rice and particularly in two-line hybrid rice

10.21203/rs.3.rs-42428/v1 ◽

2020 ◽

Author(s):

Qiming Lv ◽

xiuli zhang ◽

dingyang yuan ◽

zhiyuan Huang ◽

rui peng ◽

...

Keyword(s):

Resistance Gene ◽

Seed Production ◽

High Efficiency ◽

Hybrid Rice ◽

Indica Rice ◽

Rice Paddy ◽

Rice Seed ◽

Rice Varieties ◽

Broad Spectrum Resistance ◽

Allelic Variations

Abstract Background Benzobicyclon (BBC) is a β-triketone herbicide (bTH) used in rice paddy fields. It has the advantages of high efficiency, low toxicity, high crop safety, and good environmental compatibility, and shows efficacy against paddy weeds resistant to other types of herbicides. However, because BBC is not safe for some important indica rice varieties, it is currently only registered and applied in japonica rice areas. Results In this study, by analyzing haplotypes of the bTHs broad-spectrum resistance gene HIS1 and phenotypes for BBC in 493 major indica rice accessions in China, we identified a novel non-functional allelic variant of HIS1 besides the previously reported 28-bp deletion. Through detection with markers specific to the two non-functional mutations, it was clear that 25.4% of indica conventional varieties, 59.9% of restorers and 15.9% of sterile lines were susceptible to BBC. In addition, due to natural allelic variations of the HIS1 gene in sterile and restorer lines, some two-line hybrid sterile lines were sensitive to bTHs, and the corresponding restorers were resistant. We showed the potential of effectively using bTHs to solve the problem of two-line hybrid rice seed purity due to self-crossing of sterile lines during hybrid rice seed production. Finally, allelic variations of the HIS1 gene may also play an important role in the mechanized seed production of hybrid rice. Conclusions Our findings provide guidance for the application of BBC in indica rice areas, and provide a non-transgenic approach to solve the problem of seed purity of two-line hybrid rice.

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The genic nature of gamete eliminator in rice.

Genetics ◽

10.1093/genetics/125.1.183 ◽

1990 ◽

Vol 125 (1) ◽

pp. 183-191 ◽

Cited By ~ 5

Author(s):

Y Sano

Keyword(s):

Genetic Basis ◽

Hybrid Sterility ◽

Oryza Glaberrima ◽

Male Sterile ◽

Cultivated Rice ◽

Sterility Gene ◽

Wx Locus ◽

Allelic Interaction ◽

Different Genetic Background ◽

Marked Suppression

Abstract The two cultivated rice species, Oryza sativa and Oryza glaberrima, are morphologically alike but are reproductively isolated from each other by hybrid sterility. The hybrid is male sterile but partially female fertile. Backcross experiments were conducted to introduce an alien factor controlling hybrid sterility from O. glaberrima (W025) into O. sativa (T65wx) and examine the genetic basis. An extracted sterility factor, closely linked to the wx locus, induced gametic abortion due to allelic interaction and was tentatively designated as S(t). The segregation patterns for infertility was explained by assuming that W025 and T65wx carried S(t) and S(t)a, respectively, and gametes with S(t)a aborted only in the heterozygote (S(t)/S(t)a) although the elimination of female gametes was incomplete. Thus, S(t) seemed to be intermediate between a gamete eliminator and pollen killer. However, S(t) was proven to be likely the same as S1 which was formerly reported as gamete eliminator in a different genetic background of O. sativa. In addition, a chromosomal segment containing S1 (or S(t] caused a marked suppression of crossing over around it, suggesting the presence of an inversion. Further, female transmission of S1a increased as the segment containing S1 became small by recombination. After S1 was further purified by successive backcrosses up to the BC15 generation, it became pollen killer. The present results give evidence that a profound sterility gene such as gamete eliminator can be made from accumulation of pollen killer and its modifier(s) when pollen killer and modifier(s) are linked, they behave as a gene complex in the hybrid.

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Exploring natural allelic variations of the β-triketone herbicide resistance gene HIS1 for application in indica rice and particularly in two-line hybrid rice

10.21203/rs.3.rs-42428/v3 ◽

2020 ◽

Author(s):

Qiming Lv ◽

Xiuli Zhang ◽

Dingyang Yuan ◽

Zhiyuan Huang ◽

Rui Peng ◽

...

Keyword(s):

Resistance Gene ◽

Seed Production ◽

High Efficiency ◽

Hybrid Rice ◽

Indica Rice ◽

Rice Paddy ◽

Rice Seed ◽

Rice Varieties ◽

Allelic Variations ◽

Fertility Restorers

Abstract Background: Benzobicyclon (BBC) is a β-triketone herbicide (bTH) used in rice paddy fields. It has the advantages of high efficiency, low toxicity, high crop safety, and good environmental compatibility, and shows efficacy against paddy weeds resistant to other types of herbicides. However, as some important indica rice varieties are susceptible to BBC, BBC is currently only registered and applied in japonica rice cultivation areas.Results: By analyzing haplotypes of the bTHs broad-spectrum resistance gene HIS1 and phenotypes for BBC in 493 major indica rice accessions in China, we identified a novel non-functional allelic variant of HIS1 in addition to the previously reported 28-bp deletion. Through detection with markers specific to the two non-functional mutations, it was clear that 25.4% of indica conventional varieties, 59.9% of fertility restorers, and 15.9% of sterile lines were susceptible to BBC. In addition, due to natural allelic variations of the HIS1 gene in the sterile and restorer lines, some two-line hybrid sterile lines were sensitive to bTHs, and the corresponding restorers were resistant. We showed the potential effectiveness of using bTHs to address the issue of two-line hybrid rice seed purity stemming from the self-crossing of sterile lines during hybrid rice seed production. Finally, allelic variations of the HIS1 gene may also play an important role in the mechanized seed production of hybrid rice.Conclusions: Our findings offer guidance for the application of BBC in indica rice areas and provide a non-transgenic approach to address the seed purity issue of two-line hybrid rice.

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Understanding and breaking down the reproductive barrier between Asian and African cultivated rice: a new start for hybrid rice breeding

Science China Life Sciences ◽

10.1007/s11427-019-9592-6 ◽

2019 ◽

Vol 62 (8) ◽

pp. 1114-1116 ◽

Cited By ~ 2

Author(s):

Yidan Ouyang

Keyword(s):

Hybrid Rice ◽

Reproductive Barrier ◽

Rice Breeding ◽

Cultivated Rice

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Evolution of the Wx genotype combination in hybrid rice

10.21203/rs.2.18052/v1 ◽

2019 ◽

Author(s):

bingran Zhao ◽

Ye Shao ◽

Yan Peng ◽

Bigang Mao ◽

Qiming Lv ◽

...

Keyword(s):

Hybrid Rice ◽

Allelic Variation ◽

Amylose Content ◽

Major Gene ◽

Eating Quality ◽

Sequencing Data ◽

Genotype Combination ◽

Synonymous Mutations ◽

Allelic Variations

Abstract Background: With increased interest in the quality characteristics of hybrid rice, its quality traits have received a certain extent of improvement. However, comparisons to high-quality conventional rice, especially its eating quality, have revealed that more work is still required. Amylose content is a key determinant of the eating quality of rice, and Wx , the major gene controlling amylose content, has many allelic variants. A complete understanding of the Wx allelic variations in cultivated rice and the evolution process of the Wx genotype in hybrid rice are the premises for the rational utilization of rich genetic resources in the quality breeding of hybrid rice. Based on the 3K RGP re-sequencing data, we sought to analyse the allelic variation at the Wx locus and develop a set of Kompetitive Allele-Specific PCR markers. Furthermore, we used the markers to analyse the evolution of a combination of the Wx genotype in hybrid rice.Results: Eight known alleles existing globally were identified, and their evident regional preferences and Indica - japonica background differences were revealed. An additional five non-synonymous mutations were identified in the coding region of the Wx gene for the first time, including a new functional site located in the active centre of OsGBSS1. By genotyping the basic hybrid parents obtained from 1976 to 2018, we found that only three Wx allelic variations existed. Wx lv was widely used in the female parents of the three-line hybrid rice, and Wx a was used in the female parents of early two-line hybrid rice; however, they were gradually replaced by Wx b .Conclusions: In this study, the Wx lv allele was found to be the cause of the poor eating quality of early hybrid rice. With the elimination of the Wx lv allele and introduction of Wx b in both parents, the eating quality of hybrid rice was generally improved. Only three allelic variations were present in the previous hybrid rice. For further eating quality improvement of hybrid rice, more Wx alleles should be introduced.

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Exploring natural allelic variations of the β-triketone herbicide resistance gene HIS1 for application in indica rice and particularly in two-line hybrid rice

10.21203/rs.3.rs-42428/v4 ◽

2020 ◽

Author(s):

Qiming Lv ◽

xiuli zhang ◽

dingyang yuan ◽

zhiyuan Huang ◽

rui peng ◽

...

Keyword(s):

Resistance Gene ◽

Seed Production ◽

High Efficiency ◽

Hybrid Rice ◽

Indica Rice ◽

Rice Paddy ◽

Rice Seed ◽

Rice Varieties ◽

Allelic Variations ◽

Fertility Restorers

Abstract Background: Benzobicyclon (BBC) is a β-triketone herbicide (bTH) used in rice paddy fields. It has the advantages of high efficiency, low toxicity, high crop safety, and good environmental compatibility, and shows efficacy against paddy weeds resistant to other types of herbicides. However, as some important indica rice varieties are susceptible to BBC, BBC is currently only registered and applied in japonica rice cultivation areas.Results: By analyzing haplotypes of the bTHs broad-spectrum resistance gene HIS1 and phenotypes for BBC in 493 major indica rice accessions in China, we identified a novel non-functional allelic variant of HIS1 in addition to the previously reported 28-bp deletion. Through detection with markers specific to the two non-functional mutations, it was clear that 25.4% of indica conventional varieties, 59.9% of fertility restorers, and 15.9% of sterile lines were susceptible to BBC. In addition, due to natural allelic variations of the HIS1 gene in the sterile and restorer lines, some two-line hybrid sterile lines were sensitive to bTHs, and the corresponding restorers were resistant. We showed the potential effectiveness of using bTHs to address the issue of two-line hybrid rice seed purity stemming from the self-crossing of sterile lines during hybrid rice seed production. Finally, allelic variations of the HIS1 gene may also play an important role in the mechanized seed production of hybrid rice.Conclusions: Our findings offer guidance for the application of BBC in indica rice areas and provide a non-transgenic approach to address the seed purity issue of two-line hybrid rice.

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Exploring natural allelic variations of the β-triketone herbicide resistance gene HIS1 for application in indica rice and particularly in two-line hybrid rice

10.21203/rs.3.rs-42428/v2 ◽

2020 ◽

Author(s):

Qiming Lv ◽

Xiuli Zhang ◽

Dingyang Yuan ◽

Zhiyuan Huang ◽

Rui Peng ◽

...

Keyword(s):

Resistance Gene ◽

Seed Production ◽

High Efficiency ◽

Hybrid Rice ◽

Indica Rice ◽

Rice Paddy ◽

Rice Seed ◽

Rice Varieties ◽

Broad Spectrum Resistance ◽

Allelic Variations

Abstract Background: Benzobicyclon (BBC) is a β-triketone herbicide (bTH) used in rice paddy fields. It has the advantages of high efficiency, low toxicity, high crop safety, and good environmental compatibility, and shows efficacy against paddy weeds resistant to other types of herbicides. However, as some important indica rice varieties are susceptible to BBC, BBC is currently only registered and applied in japonica rice cultivation areas.Results: By analyzing haplotypes of the bTHs broad-spectrum resistance gene HIS1 and phenotypes for BBC in 493 major indica rice accessions in China, we identified a novel non-functional allelic variant of HIS1 in addition to the previously reported 28-bp deletion. Through detection with markers specific to the two non-functional mutations, it was clear that 25.4% of indica conventional varieties, 59.9% of restorers, and 15.9% of sterile lines were susceptible to BBC. In addition, due to natural allelic variations of the HIS1 gene in the sterile and restorer lines, some two-line hybrid sterile lines were sensitive to bTHs, and the corresponding restorers were resistant. We showed the potential effectiveness of using bTHs to address the issue of two-line hybrid rice seed purity stemming from the self-crossing of sterile lines during hybrid rice seed production. Finally, allelic variations of the HIS1 gene may also play an important role in the mechanized seed production of hybrid rice.Conclusions: Our findings offer guidance for the application of BBC in indica rice areas and provide a non-transgenic approach to address the seed purity issue of two-line hybrid rice.

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