scholarly journals Two SNP Mutations Turned off Seed Shattering in Rice

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 475
Author(s):  
Yu Zhang ◽  
Jiawu Zhou ◽  
Ying Yang ◽  
Walid Hassan Elgamal ◽  
Peng Xu ◽  
...  
Keyword(s):  
Ssr Marker ◽  
Wild Relatives ◽  
Ancestral Haplotype ◽  
Recurrent Parent ◽  
Isogenic Line ◽  
Chromosome 4 ◽  
Cultivated Rice ◽  
Japonica Variety ◽  
Seed Shattering ◽  
Shed Light

Seed shattering is an important agronomic trait in rice domestication. In this study, using a near-isogenic line (NIL-hs1) from Oryza barthii, we found a hybrid seed shattering phenomenon between the NIL-hs1 and its recurrent parent, a japonica variety Yundao 1. The heterozygotes at hybrid shattering 1 (HS1) exhibited the shattering phenotype, whereas the homozygotes from both parents conferred the non-shattering. The causal HS1 gene for hybrid shattering was located in the region between SSR marker RM17604 and RM8220 on chromosome 4. Sequence verification indicated that HS1 was identical to SH4, and HS1 controlled the hybrid shattering due to harboring the ancestral haplotype, the G allele at G237T site and C allele at C760T site from each parent. Comparative analysis at SH4 showed that all the accessions containing ancestral haplotype, including 78 wild relatives of rice and 8 African cultivated rice, had the shattering phenotype, whereas all the accessions with either of the homozygous domestic haplotypes at one of the two sites, including 17 wild relatives of rice, 111 African cultivated rice and 65 Asian cultivated rice, showed the non-shattering phenotype. Dominant complementation of the G allele at G237T site and the C allele at C760T site in HS1 led to a hybrid shattering phenotype. These results help to shed light on the nature of seed shattering in rice during domestication and improve the moderate shattering varieties adapted to mechanized harvest.

Red Rice (Oryza sativa) Biology. I. Characterization of Red Rice Ecotypes

1999 ◽  
Vol 13 (1) ◽  
pp. 12-18 ◽  
Author(s):  
José A. Noldin ◽  
James M. Chandler ◽  
Garry N. McCauley
Keyword(s):  
Flag Leaf ◽  
Natural Hybridization ◽  
Rice Cultivars ◽  
Red Rice ◽  
Cultivated Rice ◽  
Seed Shattering ◽  
Seed Moisture ◽  
Biology I ◽  
Plant Characteristics

Plant characteristics of red rice ecotypes obtained from Arkansas, Louisiana, Mississippi, and Texas, including 11 strawhulled, five blackhulled, two goldhulled, and one brownhulled type, were evaluated under field conditions. Most ecotypes were uniform and stable but manifested considerable genetic variability. Red rice plants had pubescent leaves, were taller with lighter green color, and produced more tillers and panicles per plant than rice cultivars ‘Lemont,’ ‘Mars,’ and ‘Maybelle.’ Most ecotypes were highly susceptible to seed shattering starting about 14 d after anthesis when seed moisture was more than 25%. Seeds of most ecotypes were highly dormant at harvest. Rice cultivars had a larger flag leaf and more total leaf area per plant at anthesis and produced more seeds per panicle than red rice. Some red rice ecotypes had plant characteristics closely related to cultivated rice suggesting natural hybridization with rice.

scholarly journals Contribution of Wild Relatives to Durum Wheat (Triticum turgidum subsp. durum) Yield Stability across Contrasted Environments

Agronomy ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1992
Author(s):  
Hafid Aberkane ◽  
Ahmed Amri ◽  
Bouchra Belkadi ◽  
Abdelkarim Filali-Maltouf ◽  
Jan Valkoun ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Triticum Turgidum ◽  
Wild Relatives ◽  
Yield Stability ◽  
Yield Potential ◽  
High Yield ◽  
Interspecific Crosses ◽  
Aegilops Speltoides ◽  
Recurrent Parent ◽  
Environment Interaction

Durum wheat (Triticum turgidum subsp. durum) is mostly grown in Mediterranean type environments, characterized by unpredictable rainfall amounts and distribution, heat stress, and prevalence of major diseases and pests, all to be exacerbated with climate change. Pre-breeding efforts transgressing adaptive genes from wild relatives need to be strengthened to overcome these abiotic and biotic challenges. In this study, we evaluated the yield stability of 67 lines issued from interspecific crosses of Cham5 and Haurani with Triticum dicoccoides, T. agilopoides, T. urartu, and Aegilops speltoides, grown under 15 contrasting rainfed and irrigated environments in Morocco, and heat-prone conditions in Sudan. Yield stability was assessed using parametric (univariate (e.g., Bi, S2di, Pi etc) and multivariate (ASV, SIPC)) and non-parametric (Si1, Si2, Si3 and Si6) approaches. The combined analysis of variance showed the highly significant effects of genotypes, environments, and genotype-by-environment interaction (GEI). The environments varied in yield (1370–6468 kg/ha), heritability (0.08–0.9), and in their contribution to the GEI. Several lines derived from the four wild parents combined productivity and stability, making them suitable for unpredictable climatic conditions. A significant advantage in yield and stability was observed in Haurani derivatives compared to their recurrent parent. Furthermore, no yield penalty was observed in many of Cham5 derivatives; they had improved yield under unfavorable environments while maintaining the high yield potential from the recurrent parent (e.g., 142,026 and 142,074). It was found that a limited number of backcrosses can produce high yielding/stable germplasm while increasing diversity in a breeding pipeline. Comparing different stability approaches showed that some of them can be used interchangeably; others can be complementary to combine broad adaption with higher yield.

scholarly journals Wxlv, the Ancestral Allele of Rice Waxy Gene

Proceedings ◽  
2020 ◽  
Vol 36 (1) ◽  
pp. 140 ◽  
Author(s):  
Changquan Zhang ◽  
Jihui Zhu ◽  
Shengjie Chen ◽  
Qiaoquan Liu
Keyword(s):  
Amylose Content ◽  
Waxy Gene ◽  
Evolutionary Analysis ◽  
Ancestral Allele ◽  
Cultivated Rice ◽  
Functional Sites ◽  
Wx Locus ◽  
Wx Gene ◽  
Shed Light

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.

scholarly journals Molecular Mapping of YrSP and Its Relationship with Other Genes for Stripe Rust Resistance in Wheat Chromosome 2BL

2015 ◽  
Vol 105 (9) ◽  
pp. 1206-1213 ◽  
Author(s):  
J. Y. Feng ◽  
M. N. Wang ◽  
X. M. Chen ◽  
D. R. See ◽  
Y. L. Zheng ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Chromosomal Location ◽  
Molecular Mapping ◽  
Puccinia Striiformis ◽  
Dominant Gene ◽  
The United States ◽  
Stripe Rust Resistance ◽  
Recurrent Parent ◽  
Isogenic Line ◽  
Sts Markers

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of wheat worldwide. Resistance is the best way to control the disease. YrSP, a gene originally from ‘Spaldings Prolific’ wheat and providing resistance to a broad spectrum of races, is used for differentiating P. striiformis f. sp. tritici races but its chromosomal location is not clear. To map YrSP, a near-isogenic line (AvSYrSPNIL) was backcrossed to the recurrent parent, Avocet S. Genetic analysis of the BC7F1, BC8, BC7F2, and BC7F3 progenies confirmed a single dominant gene for resistance. In total, 182 BC7F2 plants and their derived BC7F3 lines were phenotyped with an avirulent P. striiformis f. sp. tritici race and genotyped with simple-sequence repeat (SSR), single-nucleotide polymorphism (SNP), and sequence-tagged site (STS) markers. A linkage map was constructed with 3 SSR, 17 SNP, and 3 STS markers covering 23.3 centimorgans (cM). Markers IWA638 and dp269 were 0.6 cM proximal and 1.5 cM distal, respectively, to YrSP. The gene was mapped in chromosome bin 2BL-C-0.5, physically within the proximal 50% of the chromosome 2BL arm. Allelism tests based on F2 phenotypes indicated that YrSP is closely linked to but not allelic with genes Yr5, Yr7, Yr43, Yr44, and Yr53. Infection type data from tests with 10 historical and currently predominant P. striiformis f. sp. tritici races in the United States also demonstrated differences in specificity between YrSP and the other genes. The specificity of YrSP is useful in differentiating P. striiformis f. sp. tritici races and studying the plant–pathogen interactions, and the information of chromosomal location of the gene and its tightly linked markers should be useful in developing resistant cultivars when combined with other genes for resistance to stripe rust.

scholarly journals Variations of Floral Traits in Asian Cultivated Rice (Oryza sativa L.) and its Wild Relatives (O. rufipogon Griff.)

2003 ◽  
Vol 53 (4) ◽  
pp. 345-352 ◽  
Author(s):  
Yusaku Uga ◽  
Yoshimichi Fukuta ◽  
Ryo Ohsawa ◽  
Tatsuhito Fujimura
Keyword(s):  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Wild Relatives ◽  
Floral Traits ◽  
Cultivated Rice

scholarly journals Control of Thousand-Grain Weight by OsMADS56 in Rice

2021 ◽  
Vol 23 (1) ◽  
pp. 125
Author(s):  
Zi-Wei Zuo ◽  
Zhen-Hua Zhang ◽  
De-Run Huang ◽  
Ye-Yang Fan ◽  
Si-Bin Yu ◽  
...  
Keyword(s):  
Haplotype Analysis ◽  
Molecular Design ◽  
Grain Weight ◽  
Major Type ◽  
Isogenic Line ◽  
Thousand Grain Weight ◽  
Cultivated Rice ◽  
Knock Out ◽  
New Gene ◽  
Trait Locus

Grain weight and size are important traits determining grain yield and influencing grain quality in rice. In a previous study, a quantitative trait locus controlling thousand-grain weight (TGW) in rice, qTGW10-20.8, was mapped in a 70.7 kb region on chromosome 10. Validation of the candidate gene for qTGW10-20.8, OsMADS56 encoding a MADS-box transcription factor, was performed in this study. In a near-isogenic line (NIL) population segregated only at the OsMADS56 locus, NILs carrying the OsMADS56 allele of IRBB52 were 1.9% and 2.9% lower in TGW than NILs carrying the OsMADS56 allele of Teqing in 2018 and 2020, respectively. Using OsMADS56 knock-out mutants and overexpression transgenic plants, OsMADS56 was validated as the causal gene for qTGW10-20.8. Compared with the recipients, the TGW of the mutants was reduced by 6.0–15.0%. In these populations, decreased grain weight and size were associated with a reduction in the expression of OsMADS56. In transgenic populations of OsMADS56 driven by a strong constitutive promoter, grain weight and size of the positive plants were significantly higher than those of the negative plants. Haplotype analysis showed that the Teqing-type allele of OsMADS56 is the major type presented in cultivated rice and used in variety improvement. Cloning of OsMADS56 provides a new gene resource to improve grain weight and size through molecular design breeding.

scholarly journals Identification of Rice Large Grain Gene GW2 by Whole-Genome Sequencing of a Large Grain-Isogenic Line Integrated with Japonica Native Gene and Its Linkage Relationship with the Co-integrated Semidwarf Gene d60 on Chromosome 2

2019 ◽  
Vol 20 (21) ◽  
pp. 5442
Author(s):  
Motonori Tomita ◽  
Shiho Yazawa ◽  
Yoshimasa Uenishi
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rice Variety ◽  
Kernel Weight ◽  
Snp Markers ◽  
Recurrent Parent ◽  
Whole Genome ◽  
Isogenic Line ◽  
Chromosome 2 ◽  
Single Nucleotide

Genetic analysis of “InochinoIchi,” an exceptionally large grain rice variety, was conducted through five continuous backcrosses with Koshihikari as a recurrent parent using the large grain F3 plant in Koshihikari × Inochinoichi as a nonrecurrent parent. Thorough the F2 and all BCnF2 generations, large, medium, and small grain segregated in a 1:2:1 ratio, indicating that the large grain is controlled by a single allele. Mapping by using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers with small grain homozygous segregants in the F2 of Nipponbare × Inochinoichi, revealed linkage with around 7.7 Mb markers from the distal end of the short arm of chromosome 2. Whole-genome sequencing on a large grain isogenic Koshihikari (BC4F2) using next-generation sequencing (NGS) identified a single nucleotide deletion in GW2 gene, which is located 8.1 Mb from the end of chromosome 2, encoding a RING protein with E3 ubiquitin ligase activity. The GW2-integrated isogenic Koshihikari showed a 34% increase in thousand kernel weight compared to Koshihikari, while retaining a taste score of 80. We further developed a large grain/semi-dwarf isogenic Koshihikari integrated with GW2 and the semidwarfing gene d60, which was found to be localized on chromosome 2. The combined genotype secured high yielding while providing robustness to withstand climate change, which can contribute to the New Green Revolution.

Discordant Patterns of Introgression Suggest Historical Gene Flow into Thai Weedy Rice from Domesticated and Wild Relatives

2019 ◽  
Vol 110 (5) ◽  
pp. 601-609 ◽  
Author(s):  
Marshall J Wedger ◽  
Tonapha Pusadee ◽  
Anupong Wongtamee ◽  
Kenneth M Olsen
Keyword(s):  
Gene Flow ◽  
Ssr Markers ◽  
Wild Rice ◽  
Allelic Variation ◽  
Wild Relatives ◽  
Weedy Rice ◽  
Cultivated Rice ◽  
Crop Species ◽  
Global Food Security ◽  
North East

Abstract Weedy relatives of crop species infest agricultural fields worldwide, reducing harvests and threatening global food security. These weeds can potentially evolve and adapt through gene flow from both domesticated crop varieties and reproductively compatible wild relatives. We studied populations of weedy rice in Thailand to investigate the role of introgression from cultivated and wild rice in their evolution. We examined 2 complementary sources of genetic data: allelic variation at 3 rice domestication genes (Bh4, controlling hull color; Rc, controlling pericarp color and seed dormancy; and sh4, controlling seed shattering), and 12 previously published SSR markers. Sampling spanned 3 major rice growing regions in Thailand (Lower North, North East, and Central Plain) and included 124 cultivated rice accessions, 166 weedy rice accessions, and 98 wild rice accessions. Weedy rice strains were overall closely related to the cultivated varieties with which they co-occur. Domestication gene data revealed potential adaptive introgression of sh4 shattering alleles from wild rice. Introgression of potentially maladaptive rc crop alleles (conferring reduced dormancy) was also detected, with the frequency of the crop allele highest in northern populations. Although SSR markers also indicated introgression into weed populations from wild and cultivated rice, there was little overlap with domestication genes in the accessions showing admixed ancestry. This suggests that much of the introgression we detected at domestication genes most likely reflects past introgression rather than recent gene flow. This finding has implications for understanding long-term gene flow dynamics between rice and its weedy and wild relatives, including potential risks of transgene escape.

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