Fangming Xie - Academia.edu (original) (raw)

Papers by Fangming Xie

Research paper thumbnail of Shanyou 63: an elite mega rice hybrid in China

Rice

Hybrid rice has been successfully used for commercial rice production for 40 years in China. Shan... more Hybrid rice has been successfully used for commercial rice production for 40 years in China. Shanyou 63, a mega rice hybrid, derived from the parents Zhenshan 97A and Minghui 63, was a milestone for China's hybrid rice development and production because of its high yield and wide adaptability. It was planted in 16 provinces of the country on 17% of the national hybrid rice area annually during the 29 years from 1984 to 2012. The hybrid and its parents have also been widely used for basic and agronomic studies related to rice heterosis, stress tolerance, molecular markers and genomics. We review the development of the hybrid and its parents and their major characteristics for the purpose of learning from the history and guiding future hybrid rice development. The history and development experience show that a successful hybrid rice variety should have multiple traits, including high yield, wide adaptability, resistances to major diseases, and high rice quality that meets the demands of consumers. From the breeding aspect, hybrid rice provides the advantage of combining elite traits or genes from different types of parents, such as those from subspecies of indica and japonica, into a single variety. Farmers prefer not only a variety with high yield potential, but also stable yields and local adaptability.

Research paper thumbnail of Genetic Effects of Wx Allele Combinations on Apparent Amylose Content in Tropical Hybrid Rice

Research paper thumbnail of Hybrid rice: achievement, challenges and opportunity

Research paper thumbnail of Genome-wide association study of outcrossing in cytoplasmic male sterile lines of rice

Scientific reports, Jan 12, 2017

Stigma exsertion and panicle enclosure of male sterile lines are two key determinants of outcross... more Stigma exsertion and panicle enclosure of male sterile lines are two key determinants of outcrossing in hybrid rice seed production. Based on 43,394 single nucleotide polymorphism markers, 217 cytoplasmic male sterile lines were assigned into two subpopulations and a mixed-group where the linkage disequilibrium decay distances varied from 975 to 2,690 kb. Genome-wide association studies (GWAS) were performed for stigma exsertion rate (SE), panicle enclosure rate (PE) and seed-setting rate (SSR). A total of 154 significant association signals (P < 0.001) were identified. They were situated in 27 quantitative trait loci (QTLs), including 11 for SE, 6 for PE, and 10 for SSR. It was shown that six of the ten QTLs for SSR were tightly linked to QTLs for SE or/and PE with the expected allelic direction. These QTL clusters could be targeted to improve the outcrossing of female parents in hybrid rice breeding. Our study also indicates that GWAS-base QTL mapping can complement and enhance...

Research paper thumbnail of History and prospects of hybrid rice development outside of China

Chinese Science Bulletin, 2016

Research paper thumbnail of Rice cultivar R031001

Research paper thumbnail of Identification of stable QTLs causing chalk in rice grains in nine environments

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, Jan 24, 2015

A novel QTL cluster for chalkiness on Chr04 was identified using single environment analysis and ... more A novel QTL cluster for chalkiness on Chr04 was identified using single environment analysis and joint mapping across 9 environments in Asia and South American. QTL NILs showed that each had a significant effect on chalk. Chalk in rice grains leads to a significant loss in the proportion of marketable grains in a harvested crop, leading to a significant financial loss to rice farmers and traders. To identify the genetic basis of chalkiness, two sets of recombinant inbred lines (RILs) derived from reciprocal crosses between Lemont and Teqing were used to find stable QTLs for chalkiness. The RILs were grown in seven locations in Asia and Latin American and in two controlled environments in phytotrons. A total of 32 (21) and 46 (22) QTLs for DEC and PGWC, most of them explaining more than 10 % of phenotypic variation, were detected based on single environment analysis in T/L (L/T) population, respectively. Seven (2) and 7 (3) QTLs for DEC and PGWC were identified in the T/L (L/T) popul...

Research paper thumbnail of Grain yield and quality responses of tropical hybrid rice to high night-time temperature

Field Crops Research, 2015

Research paper thumbnail of Heterotic groups of tropical indica rice germplasm

Theoretical and Applied Genetics, 2014

Four heterotic groups were identified for tropical indica rice germplasm to develop hybrid rice i... more Four heterotic groups were identified for tropical indica rice germplasm to develop hybrid rice in the tropics based on two studies. Heterotic groups are of fundamental importance in hybrid crop breeding. This study investigated hybrid yield, yield heterosis and combining ability within and among groups based on genetic distance derived from single-nucleotide polymorphism markers. The main objectives of the study were to (1) evaluate the magnitude of yield heterosis among marker-based groups, (2) identify possible heterotic groups for tropical indica hybrid rice, and (3) validate heterotic patterns concluded from a previous study. Seventeen rice parents selected from improved indica germplasm from the tropics with high genetic divergence and 136 derived hybrids were evaluated in five environments. The hybrids had more yield than their parents with an average of 24.1 % mid-parent heterosis. Genotype × environment interaction was the major factor affecting variations in yield and yield heterosis, which raised a necessity and a challenge to develop heterotic rice hybrid adapted to different regions and seasons in the tropics. Yield, yield heterosis and combining ability were significantly increased in inter-group than in intra-group hybrids. Four heterotic groups and three promising hybridization patterns, which could be used in tropical hybrid rice breeding, were identified based on marker-based grouping, yield and yield heterosis analyses in the two studies. The study reveals that molecular markers analysis can serve as a basis for assigning germplasm into heterotic groups and to provide guidelines for parental selection in hybrid rice breeding.

Research paper thumbnail of Determination of heterotic groups for tropical Indica hybrid rice germplasm

Theoretical and Applied Genetics, 2014

were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis amo... more were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis among marker-based parental groups, (2) examining the consistency between marker-based group and heterotic performance of hybrids, and (3) identifying foundational hybrid parents in discrete germplasm pools to provide a reference for tropical indica hybrid rice breeding. Significant differences in yield, yield heterosis and combining ability were detected among parents and among hybrids. On average, the hybrids yielded 14.8 % higher than the parents. results revealed that intergroup hybrids yielded higher, with higher yield heterosis than intra-group hybrids. Four heterotic patterns within two heterotic groups based on current IrrI Band r-line germplasm were identified. Parents in two marker-based groups were identified with limited breeding value among current IrrI hybrid rice germplasm because of their lowest contribution to heterotic hybrids. Heterotic hybrids are significantly correlated with high-yielding parents. The efficiency of breeding heterotic hybrids could be enhanced using selected parents within identified marker-based heterotic groups. This information is useful for exploiting those widely distributed IrrI hybrid rice parents.

Research paper thumbnail of Genetic diversity and structure of improved indica rice germplasm

Plant Genetic Resources, 2014

The characterization of genetic diversity and structure for improved cultivated varieties/elite l... more The characterization of genetic diversity and structure for improved cultivated varieties/elite lines is tremendously important to assist breeders in parental selection for inbred and hybrid breeding and heterotic group construction. In this study, a total of 737 improvedindicavarieties/lines developed recently and/or widely used by presentindicabreeding programmes worldwide were genotyped with a 384-single-nucleotide polymorphism assay. Model-based population structure analysis revealed the presence of two major groups with six subgroups (SGs), wherein no clear correlation was found between the groups/SGs and breeding programmes or geographical origin of the accessions. Over half of the accessions (51.8%) appeared to have less than 0.6 memberships assigned to any one of the six model-based groups, highlighting the wide range of gene flow within improvedindicavarieties/lines and the genetic integration of valuable alleles shared by ancestries among improved high-yielding varieties/l...

Research paper thumbnail of Genetic diversity and structure of indica rice varieties from two heterotic pools of southern China and IRRI

Plant Genetic Resources, 2012

Investigation of genetic diversity and the relationships among varieties and breeding lines is of... more Investigation of genetic diversity and the relationships among varieties and breeding lines is of great importance to facilitate parental selection in the development of inbred and hybrid rice varieties and in the construction of heterotic groups. The technology of single nucleotide polymorphism (SNP) is being advanced for the assessment of population diversity and genetic structures. We characterized 215 widely cultivatedindicarice varieties developed in southern China and at the International Rice Research Institute (IRRI) using IRRI-developed SNP oligonucleotide pooled assay (OPA) to provide grouping information of rice mega-varieties for further heterotic pool study. The results revealed that the Chinese varieties were more divergent than the IRRI varieties. Two major subpopulations were clustered for the varieties using a model-based grouping method. The IRRI varieties were closely grouped and separated clearly from the majority of the Chinese varieties. The Chinese varieties w...

Research paper thumbnail of Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors

Nucleic Acids Research, 2010

Many genes exist in the form of families; however, little is known about their size variation, ev... more Many genes exist in the form of families; however, little is known about their size variation, evolution and biology. Here, we present the size variation and evolution of the nucleotide-binding site (NBS)encoding gene family and receptor-like kinase (RLK) gene family in Oryza, Glycine and Gossypium. The sizes of both families vary by numeral fold, not only among species, surprisingly, also within a species. The size variations of the gene families are shown to correlate with each other, indicating their interactions, and driven by natural selection, artificial selection and genome size variation, but likely not by polyploidization. The numbers of genes in the families in a polyploid species are similar to those of one of its diploid donors, suggesting that polyploidization plays little roles in the expansion of the gene families and that organisms tend not to maintain their 'surplus' genes in the course of evolution. Furthermore, it is found that the size variations of both gene families are associated with organisms' phylogeny, suggesting their roles in speciation and evolution. Since both selection and speciation act on organism's morphological, physiological and biological variation, our results indicate that the variation of gene family size provides a source of genetic variation and evolution.

Research paper thumbnail of Hybrid rice heterosis and genetic diversity of IRRI and Lao rice

Field Crops Research, 2010

Research paper thumbnail of Hybrid rice performance in environments of increasing drought severity

Field Crops Research, 2012

Hybrid rice provides an option for achieving high yield potential under favorable conditions, but... more Hybrid rice provides an option for achieving high yield potential under favorable conditions, but the performance of hybrids under drought stress has not yet been fully evaluated. This study explored the feasibility of using hybrid rice technology in drought-prone rainfed lowland fields. Hybrid lines, parental inbreds, and cultivated varieties as checks were screened for yield potential in well-watered fields and for drought resistance in drained fields at different stress levels. Nineteen out of 45 hybrid lines showed a yield advantage (on average 20%) over check lines in the three well-watered environments. Classifications of drought stress levels were based on the yield reduction relative to the well-watered environments, with moderate, severe, and very severe stress levels resulting in 54%, 77% and 89% reductions in yield, respectively. The relationship between yield advantage of hybrids and drought severity differed among lines; some hybrids showed more of an advantage under severe drought, whereas others had a greater yield advantage under moderate stress. Some hybrids did not perform as well as parents under drought. In general, the harvest index of hybrids was greater than those of inbred parents and checks, and showed strong correlation with grain yield in the different stress environments. Total dry matter yield of hybrids was correlated with improved yield in all stress environments during dry seasons, and some droughttolerant hybrids also showed greater tillering efficiency and thousand-grain weight. Twenty-four selected hybrid lines were divided into seven clusters on the basis of yield trends across different drought stress environments. Among the hybrid rice lines, one cluster including IR81954H, IR81955H, and IR81956H stood out as combining high yield potential in both well-watered and drought stress environments. Hybrid IR81954H showed an 8% yield advantage over other hybrids across all studies, as well as stable yield in all the stress environments having an average yield advantage of 22% over other hybrids averaged across drought environments. These results highlight the variability among hybrids in their drought response, and the need for screening of hybrids and parents under drought stress conditions.

Research paper thumbnail of Hybrid rice heterosis and genetic diversity of IRRI and Lao rice

Field Crops Research, 2010

Glutinous and non-glutinous rice hybrids derived from IRRI and Lao PDR rice germplasm were evalua... more Glutinous and non-glutinous rice hybrids derived from IRRI and Lao PDR rice germplasm were evaluated for yield heterosis and genetic diversity based on SSR markers. Pollen and spikelet fertilities of the hybrids showed absence of effective restorer and maintainer genes in the Lao varieties for WA-CMS cytoplasm. Positive heterosis over better or male parent (Lao varieties) was observed. Hybrids derived

Research paper thumbnail of Shanyou 63: an elite mega rice hybrid in China

Rice

Hybrid rice has been successfully used for commercial rice production for 40 years in China. Shan... more Hybrid rice has been successfully used for commercial rice production for 40 years in China. Shanyou 63, a mega rice hybrid, derived from the parents Zhenshan 97A and Minghui 63, was a milestone for China's hybrid rice development and production because of its high yield and wide adaptability. It was planted in 16 provinces of the country on 17% of the national hybrid rice area annually during the 29 years from 1984 to 2012. The hybrid and its parents have also been widely used for basic and agronomic studies related to rice heterosis, stress tolerance, molecular markers and genomics. We review the development of the hybrid and its parents and their major characteristics for the purpose of learning from the history and guiding future hybrid rice development. The history and development experience show that a successful hybrid rice variety should have multiple traits, including high yield, wide adaptability, resistances to major diseases, and high rice quality that meets the demands of consumers. From the breeding aspect, hybrid rice provides the advantage of combining elite traits or genes from different types of parents, such as those from subspecies of indica and japonica, into a single variety. Farmers prefer not only a variety with high yield potential, but also stable yields and local adaptability.

Research paper thumbnail of Genetic Effects of Wx Allele Combinations on Apparent Amylose Content in Tropical Hybrid Rice

Research paper thumbnail of Hybrid rice: achievement, challenges and opportunity

Research paper thumbnail of Genome-wide association study of outcrossing in cytoplasmic male sterile lines of rice

Scientific reports, Jan 12, 2017

Stigma exsertion and panicle enclosure of male sterile lines are two key determinants of outcross... more Stigma exsertion and panicle enclosure of male sterile lines are two key determinants of outcrossing in hybrid rice seed production. Based on 43,394 single nucleotide polymorphism markers, 217 cytoplasmic male sterile lines were assigned into two subpopulations and a mixed-group where the linkage disequilibrium decay distances varied from 975 to 2,690 kb. Genome-wide association studies (GWAS) were performed for stigma exsertion rate (SE), panicle enclosure rate (PE) and seed-setting rate (SSR). A total of 154 significant association signals (P < 0.001) were identified. They were situated in 27 quantitative trait loci (QTLs), including 11 for SE, 6 for PE, and 10 for SSR. It was shown that six of the ten QTLs for SSR were tightly linked to QTLs for SE or/and PE with the expected allelic direction. These QTL clusters could be targeted to improve the outcrossing of female parents in hybrid rice breeding. Our study also indicates that GWAS-base QTL mapping can complement and enhance...

Research paper thumbnail of History and prospects of hybrid rice development outside of China

Chinese Science Bulletin, 2016

Research paper thumbnail of Rice cultivar R031001

Research paper thumbnail of Identification of stable QTLs causing chalk in rice grains in nine environments

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, Jan 24, 2015

A novel QTL cluster for chalkiness on Chr04 was identified using single environment analysis and ... more A novel QTL cluster for chalkiness on Chr04 was identified using single environment analysis and joint mapping across 9 environments in Asia and South American. QTL NILs showed that each had a significant effect on chalk. Chalk in rice grains leads to a significant loss in the proportion of marketable grains in a harvested crop, leading to a significant financial loss to rice farmers and traders. To identify the genetic basis of chalkiness, two sets of recombinant inbred lines (RILs) derived from reciprocal crosses between Lemont and Teqing were used to find stable QTLs for chalkiness. The RILs were grown in seven locations in Asia and Latin American and in two controlled environments in phytotrons. A total of 32 (21) and 46 (22) QTLs for DEC and PGWC, most of them explaining more than 10 % of phenotypic variation, were detected based on single environment analysis in T/L (L/T) population, respectively. Seven (2) and 7 (3) QTLs for DEC and PGWC were identified in the T/L (L/T) popul...

Research paper thumbnail of Grain yield and quality responses of tropical hybrid rice to high night-time temperature

Field Crops Research, 2015

Research paper thumbnail of Heterotic groups of tropical indica rice germplasm

Theoretical and Applied Genetics, 2014

Four heterotic groups were identified for tropical indica rice germplasm to develop hybrid rice i... more Four heterotic groups were identified for tropical indica rice germplasm to develop hybrid rice in the tropics based on two studies. Heterotic groups are of fundamental importance in hybrid crop breeding. This study investigated hybrid yield, yield heterosis and combining ability within and among groups based on genetic distance derived from single-nucleotide polymorphism markers. The main objectives of the study were to (1) evaluate the magnitude of yield heterosis among marker-based groups, (2) identify possible heterotic groups for tropical indica hybrid rice, and (3) validate heterotic patterns concluded from a previous study. Seventeen rice parents selected from improved indica germplasm from the tropics with high genetic divergence and 136 derived hybrids were evaluated in five environments. The hybrids had more yield than their parents with an average of 24.1 % mid-parent heterosis. Genotype × environment interaction was the major factor affecting variations in yield and yield heterosis, which raised a necessity and a challenge to develop heterotic rice hybrid adapted to different regions and seasons in the tropics. Yield, yield heterosis and combining ability were significantly increased in inter-group than in intra-group hybrids. Four heterotic groups and three promising hybridization patterns, which could be used in tropical hybrid rice breeding, were identified based on marker-based grouping, yield and yield heterosis analyses in the two studies. The study reveals that molecular markers analysis can serve as a basis for assigning germplasm into heterotic groups and to provide guidelines for parental selection in hybrid rice breeding.

Research paper thumbnail of Determination of heterotic groups for tropical Indica hybrid rice germplasm

Theoretical and Applied Genetics, 2014

were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis amo... more were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis among marker-based parental groups, (2) examining the consistency between marker-based group and heterotic performance of hybrids, and (3) identifying foundational hybrid parents in discrete germplasm pools to provide a reference for tropical indica hybrid rice breeding. Significant differences in yield, yield heterosis and combining ability were detected among parents and among hybrids. On average, the hybrids yielded 14.8 % higher than the parents. results revealed that intergroup hybrids yielded higher, with higher yield heterosis than intra-group hybrids. Four heterotic patterns within two heterotic groups based on current IrrI Band r-line germplasm were identified. Parents in two marker-based groups were identified with limited breeding value among current IrrI hybrid rice germplasm because of their lowest contribution to heterotic hybrids. Heterotic hybrids are significantly correlated with high-yielding parents. The efficiency of breeding heterotic hybrids could be enhanced using selected parents within identified marker-based heterotic groups. This information is useful for exploiting those widely distributed IrrI hybrid rice parents.

Research paper thumbnail of Genetic diversity and structure of improved indica rice germplasm

Plant Genetic Resources, 2014

The characterization of genetic diversity and structure for improved cultivated varieties/elite l... more The characterization of genetic diversity and structure for improved cultivated varieties/elite lines is tremendously important to assist breeders in parental selection for inbred and hybrid breeding and heterotic group construction. In this study, a total of 737 improvedindicavarieties/lines developed recently and/or widely used by presentindicabreeding programmes worldwide were genotyped with a 384-single-nucleotide polymorphism assay. Model-based population structure analysis revealed the presence of two major groups with six subgroups (SGs), wherein no clear correlation was found between the groups/SGs and breeding programmes or geographical origin of the accessions. Over half of the accessions (51.8%) appeared to have less than 0.6 memberships assigned to any one of the six model-based groups, highlighting the wide range of gene flow within improvedindicavarieties/lines and the genetic integration of valuable alleles shared by ancestries among improved high-yielding varieties/l...

Research paper thumbnail of Genetic diversity and structure of indica rice varieties from two heterotic pools of southern China and IRRI

Plant Genetic Resources, 2012

Investigation of genetic diversity and the relationships among varieties and breeding lines is of... more Investigation of genetic diversity and the relationships among varieties and breeding lines is of great importance to facilitate parental selection in the development of inbred and hybrid rice varieties and in the construction of heterotic groups. The technology of single nucleotide polymorphism (SNP) is being advanced for the assessment of population diversity and genetic structures. We characterized 215 widely cultivatedindicarice varieties developed in southern China and at the International Rice Research Institute (IRRI) using IRRI-developed SNP oligonucleotide pooled assay (OPA) to provide grouping information of rice mega-varieties for further heterotic pool study. The results revealed that the Chinese varieties were more divergent than the IRRI varieties. Two major subpopulations were clustered for the varieties using a model-based grouping method. The IRRI varieties were closely grouped and separated clearly from the majority of the Chinese varieties. The Chinese varieties w...

Research paper thumbnail of Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors

Nucleic Acids Research, 2010

Many genes exist in the form of families; however, little is known about their size variation, ev... more Many genes exist in the form of families; however, little is known about their size variation, evolution and biology. Here, we present the size variation and evolution of the nucleotide-binding site (NBS)encoding gene family and receptor-like kinase (RLK) gene family in Oryza, Glycine and Gossypium. The sizes of both families vary by numeral fold, not only among species, surprisingly, also within a species. The size variations of the gene families are shown to correlate with each other, indicating their interactions, and driven by natural selection, artificial selection and genome size variation, but likely not by polyploidization. The numbers of genes in the families in a polyploid species are similar to those of one of its diploid donors, suggesting that polyploidization plays little roles in the expansion of the gene families and that organisms tend not to maintain their 'surplus' genes in the course of evolution. Furthermore, it is found that the size variations of both gene families are associated with organisms' phylogeny, suggesting their roles in speciation and evolution. Since both selection and speciation act on organism's morphological, physiological and biological variation, our results indicate that the variation of gene family size provides a source of genetic variation and evolution.

Research paper thumbnail of Hybrid rice heterosis and genetic diversity of IRRI and Lao rice

Field Crops Research, 2010

Research paper thumbnail of Hybrid rice performance in environments of increasing drought severity

Field Crops Research, 2012

Hybrid rice provides an option for achieving high yield potential under favorable conditions, but... more Hybrid rice provides an option for achieving high yield potential under favorable conditions, but the performance of hybrids under drought stress has not yet been fully evaluated. This study explored the feasibility of using hybrid rice technology in drought-prone rainfed lowland fields. Hybrid lines, parental inbreds, and cultivated varieties as checks were screened for yield potential in well-watered fields and for drought resistance in drained fields at different stress levels. Nineteen out of 45 hybrid lines showed a yield advantage (on average 20%) over check lines in the three well-watered environments. Classifications of drought stress levels were based on the yield reduction relative to the well-watered environments, with moderate, severe, and very severe stress levels resulting in 54%, 77% and 89% reductions in yield, respectively. The relationship between yield advantage of hybrids and drought severity differed among lines; some hybrids showed more of an advantage under severe drought, whereas others had a greater yield advantage under moderate stress. Some hybrids did not perform as well as parents under drought. In general, the harvest index of hybrids was greater than those of inbred parents and checks, and showed strong correlation with grain yield in the different stress environments. Total dry matter yield of hybrids was correlated with improved yield in all stress environments during dry seasons, and some droughttolerant hybrids also showed greater tillering efficiency and thousand-grain weight. Twenty-four selected hybrid lines were divided into seven clusters on the basis of yield trends across different drought stress environments. Among the hybrid rice lines, one cluster including IR81954H, IR81955H, and IR81956H stood out as combining high yield potential in both well-watered and drought stress environments. Hybrid IR81954H showed an 8% yield advantage over other hybrids across all studies, as well as stable yield in all the stress environments having an average yield advantage of 22% over other hybrids averaged across drought environments. These results highlight the variability among hybrids in their drought response, and the need for screening of hybrids and parents under drought stress conditions.

Research paper thumbnail of Hybrid rice heterosis and genetic diversity of IRRI and Lao rice

Field Crops Research, 2010

Glutinous and non-glutinous rice hybrids derived from IRRI and Lao PDR rice germplasm were evalua... more Glutinous and non-glutinous rice hybrids derived from IRRI and Lao PDR rice germplasm were evaluated for yield heterosis and genetic diversity based on SSR markers. Pollen and spikelet fertilities of the hybrids showed absence of effective restorer and maintainer genes in the Lao varieties for WA-CMS cytoplasm. Positive heterosis over better or male parent (Lao varieties) was observed. Hybrids derived