Dynamic QTL Analysis on Rice Fat Content and Fat Index Using Recombinant Inbred Lines

Fat content (FC) and fat index (FI) play an important role in determining quality of eating and nutrition for rice. The objective of this study was to determine genetic information during the grain‐filling period. Seventy‐one recombinant inbred lines (RILs) derived from a cross between japonica cultivar Asominori and indica cultivar IR24 were used to analyze the developmental behavior of FC and FI by conditional and unconditional quantitative trait loci (QTL) mapping methods. At four developmental stages of grain filling, 11 unconditional QTL and 10 conditional QTL for FC as well as 11 unconditional QTL and eight conditional QTL for FI were identified. In unconditional QTL analysis, qFC‐11‐2 and qFI‐3 were consistently detected at 21 and 28 days after flowering (DAF), whereas all the conditional QTL for FC and FI could be detected at only one stage. Nine conditional and nine unconditional QTL for FC and FI were detected in the earlier three stages while three and two unconditional QTL for FC and FI, respectively, were detected in the mature stage, which suggested that more QTL could be found in the early developmental stages. The qFC‐1‐2 and qFI‐1‐2, qFC‐2‐2 and qFI‐2, qFC‐4 and qFI‐4, and qFC‐9 and qFI‐9 were located on the vicinal marker intervals. The present study suggested that accumulation of fat was governed by time‐dependent gene expression. In addition, dynamic QTL mapping might be a valid way to reveal more genetic information about the fat accumulation.     

非洲栽培稻基因渗入系粒形和剑叶形态性状的QTL定位

非洲栽培稻作为重要的水稻种质资源,其基因渗入系可以为普通栽培稻的遗传背景提供新的有利基因,如果能将这些优良基因引入普通栽培稻中,可为水稻分子设计育种提供新的基因资源。本研究以非洲栽培稻基因渗入系YIL60与轮回亲本中9B(Z9B)杂交衍生的包含188个株系的F₂和F_2:3群体为材料,对粒形性状包括粒长、粒宽、籽粒长宽比、千粒重,剑叶形态性状包括剑叶长、剑叶宽进行数量性状点位(QTL)检测。结果共检测到16个QTL,包括2个粒长QTL、3个粒宽QTL、2个籽粒长宽比QTL、2个千粒重QTL、1个剑叶长QTL、6个剑叶宽QTL,分布于第1、第6、第7、第10和第11号染色体上,贡献率为2.25%~25.64%;有4个多效性QTL区间,有4个QTL qGW7-1、qFLL10、qFLW10、qTGW7在F₂和F_2:3群体中被重复检测到,其中在第7号染色体RM3859-RM3394区间检测到同时控制粒长、粒宽、籽粒长宽比和千粒重的QTL,贡献率最高达17.10%,是一个来源于非洲栽培稻的新粒形QTL。本研究为进一步开展粒形、剑叶形态性状基因的精细定位、克隆和分子标记辅助育种工作奠定了一定的理论基础。     

Quantitative Genetic Basis of Gelatinization Temperature of Rice

Gelatinization temperature of rice starch plays an important role in grain quality. We mapped eight loci responsible for the gelatinization parameters of rice: onset temperature (T_o), peak temperature (T_p), conclusion temperature (T_c) and enthalpy (ΔH) using a population of 242 recombinant inbred lines (RIL). Eight quantitative trait loci (QTL) were mapped onto the chromosome regions where starch‐synthesis related genes are located. The Wx gene (granule‐bound starch synthase [GBSS]), and the region of chromosome 11 played major roles in gelatinization trait determination; and other loci were starch‐branching enzyme (SBE) genes that modify the two major loci by epistasis. High‐level interactions were also detected indicating a trans mode of action of the genes. The genetic basis for these parameters was consistent with the relationship between the thermal properties and the structure of the starch granule. This information can be helpful for the improvement of starch‐producing crops, including the improvement of rice grain quality, both for food and industrial uses.     

Identification of quantitative trait loci associated with shoot sodium accumulation under low potassium conditions in rice plants

Sodium (Na) application has marked beneficial effects on plant growth when the potassium (K) supply is low. Under low K supply, three japonica rice (Oryza sativa L.) cultivars, Koshihikari, Nipponbare, and Sasanishiki, accumulated more Na than three indica cultivars, IR36, IR64, and Kasalath, and the effect of Na application on growth was greater in japonica Koshihikari plants than in indica IR64 plants. A quantitative trait locus (QTL) analysis using a population of backcross inbred lines derived from japonica Koshihikari and indica Kasalath identified two significant loci associated with shoot Na concentration on chromosomes 3 and 6. The quantitative trait locus for shoot Na accumulation on chromosome 6 was confirmed in a population of chromosome segment substitution lines. The major QTL detected in this study could be useful for increasing crop productivity under low K input.     

水稻芽期耐冷性的QTL分析

本研究以98个Nipponbare／Kasalath／／Nipponbare回交重组自交家系（backcross-inbred lines,BILs）组成的群体为材料,进行水稻芽期耐冷性数量性状基因座的检测和遗传效应分析。25℃正常条件下水稻发芽7d,芽长5～10cm,5℃低温处理10d,之后升温至25℃,缓苗10d,调查活苗率,并以活苗率作为芽期耐冷性的表型值,分析亲本和98个BILs的芽期耐冷性表现。采用Windows QTL Cartographer 1．13a软件的复合区间作图法,共检测到4个苗期耐冷性数量性状基因座（quantative trait locus,QTL）,分别位于第3、第7和第12染色体上,命名为qSCT-3-1、qSCT-3～2、qSCT-7和qSCT-12。4个QTL的加性效应分别为11．16、11．14、-8.8和-14．59,可解释表型变异的12．11％,12．66％,6．82％和15．86％。     

大粒型水稻材料粒型性状的QTL定位

研究大粒型水稻材料对粒型相关基因的挖掘具有重要作用,同时也能为水稻超高产育种提供优质的种质资源。本研究以大粒型水稻材料lg1与9311杂交衍生的F2遗传分离群体为对象,分别采用2014年、2015年的粒型数据和2年的联合粒型数据,对控制其粒长、粒宽及粒厚的QTL进行初步定位。结果表明,3种情况下共定位到22个相关QTL,其中5个粒长QTL、9个粒宽QTL、8个粒厚QTL,分布于第1、第2、第3、第4、第5、第8和第11号染色体上。3种情况下均检测到QTL的有3个,即粒长QTL q GL-2-1、粒宽QTL q GW-5-1和粒厚QTL q GT-5-1,3个QTL增效等位基因均来自于亲本lg1;此外,有7个QTL在2014年、2015年和2年的联合数据定位中均被检测到,12个QTL只在1年或2年的联合数据定位中被检测到。q GL-2-1、q GW-2-3和q GT-2-3处于同一标记区间RM5812~RM13174,推测可能受同一粒型基因控制,是新的粒型QTL位点。主效QTL q GL-1-2和q GW-11-1可能是新的控制粒型QTL位点,其余检测到的QTL所在的大部分标记区间已有粒型QTL被定位或克隆。本研究结果为大粒水稻lg1粒型基因的精细定位及克隆奠定了基础。     

Quantitative Trait Loci for Brown Rice Color,Phenolics, Flavonoid Contents,and Antioxidant Capacity in Rice Grain

Phytochemicals such as phenolics and flavonoids, which are present in rice grains, are associated with reduced risk of developing chronic diseases such as cardiovascular disease, type 2 diabetes, and certain cancers. The phenolic and flavonoid compounds in rice grains also contribute to the antioxidant activity. Biofortification of rice grain by conventional breeding is one way to improve nutritional quality to combat nutritional deficiency. For improvement of the phenolics, flavonoids, and antioxidant capacity, we must understand the genetic bases of the related traits. In the present study, mapping of quantitative trait locus (QTL) for five color parameters, phenolics, flavonoids, and antioxidant capacity was completed using a composite interval mapping approach using a doubled haploid (DH) population. Correlation analysis showed that the five color parameters lightness (L*), redness (a*), yellowness (b*), chroma (C), and hue angle (H°) were intercorrelated. The phenolic content was positively correlated with the flavonoid content and antioxidant capacity (P < 0.001), whereas the flavonoid content had no relationship with antioxidant capacity, but it was positively correlated with color parameters L* and H° (P < 0.05). A total of 21 putative QTL were detected for the eight traits with at least one QTL and as many as four QTL for different traits. Three QTL at the same interval of GA285 and CT580 on chromosome 2 were significant for color parameters L*, b*, and C; the latter two traits also shared another QTL region on chromosome 8. Two QTL on chromosome 2, qPH‐2 and qFL‐2‐1, flanked by CT87 and G1234, were identified for phenolic and flavonoid content with large additive effects, explaining 16.91 and 12.71%, respectively, of the total phenotypic variation. Three QTL located at the same interval of G379A and CT360 on chromosome 7 were detected for color parameters a* and H°, and antioxidant capacity, which might be allelic to the Rd gene that is responsible for the production of the pigment in brown rice. The results of the present study may provide new opportunities for rice breeders with potential markers to improve nutritional quality by marker‐assisted selection approach.     

不同生长环境下水稻氮、磷、钾利用相关性状的QTL定位分析

【目的】鉴定影响水稻氮、磷、钾利用相关性状的QTL,为开展水稻养分高效利用分子标记辅助选择育种和肥高效基因的图位克隆提供依据。【方法】以云南强耐冷(2级)粳稻地方品种丽江新团黑谷与十和田杂交、回交获包含105个株系的孕穗期耐冷性近等基因系BC4F8及双亲为材料,在云南白邑(冷水胁迫)、寻甸(自然低温胁迫)和玉溪(正常生长环境)3种生长环境下进行水稻氮、磷、钾养分吸收相关性状的鉴定,并利用构建的含有180个SSR标记,全长为1820.6 c M,标记间平均距离为15.67 c M的遗传图谱,用基于完备区间作图法的QTL Ici Mapping V3.2软件对16个性状进行QTL定位分析。【结果】3种环境下共检测到56个QTL,分布在第1、2、3、4、5、6、7、9和10染色体上,单个性状QTL数为1~10个,单个QTL可解释的各自性状表型贡献率为8.88%~35.30%。其中,氮、磷、钾利用效率QTLs数分别为12个、27个和17个。而q TNA-1a、q TPA-1、q PHI-1、q PHI-6、q PHI-7b和q KHI-6共6个QTL在冷害和正常环境下均能检测到,稳定性较高,其贡献率变幅为10.63%~31.57%。在第1、3、4、5、6、7和10染色体上有13个标记区域存在QTL成族分布,单个QTL位点控制的性状数为2~5个,其中共同控制磷总吸收量、磷素干物质生产效率、磷素收获指数、每100 kg籽粒需钾量和钾素收获指数等性状的位点数最多。【结论】获得56个影响氮、磷、钾利用相关性状的QTL,且发现的13个QTL富集区可作为水稻氮、磷、钾高效利用分子育种的重要候选区域。     

Genome-wide association study to identify chromosomal regions related to panicle architecture in rice (Oryza sativa)

Panicle architecture directly affects the grain yield of rice; meanwhile, crop domestication has increased the complexity of rice panicle size and branching pattern. Genome-wide association study (GWAS) was performed to investigate the genetic basis underlying panicle architecture using 183 rice accessions from around the world and a 7 K SNP array. Phenotyping was conducted at Texas A&M AgriLife Research Center in Beaumont, TX. GWAS was performed using MLM (Q?+?K) model using GAPIT software. At p-value?<?0.001, a total of 49 GWAS QTLs controlling various panicle architecture traits were mapped. Considering the recurring and linked SNPs across the panicle architecture traits, 42 independent QTL regions were identified. Among these, 27 QTL regions co-localized with known genes or previously reported QTLs or significant SNP markers, while 15 were potentially novel QTL regions. The results of our study offer useful information on genetic bases controlling panicle architecture in rice, which could be further validated and utilized for designing markers for use in markers assisted selection (MAS) in rice breeding programs.

     

Quantitative Analysis of Fat Content in Rice by Near‐Infrared Spectroscopy Technique

Fat content in rice is one of the most important nutritional quality properties. But the chemical analysis of fat content is time‐consuming and costly and could result in poor reproduction between replicates. Near‐infrared spectroscopy (NIRS) can solve those problems by providing a rapid, nondestructive, and quantitative analysis. Based on the NIRS technique and partial least squares (PLS) algorithm, four calibration models were established to quantitatively analyze fat content in brown rice grain and flour and milled rice grain and flour with 248 representative samples. The determination coefficients (R²) of these calibration models were 0.79, 0.84, 0.89, and 0.91, respectively, with the corresponding root mean square errors 0.16, 0.14, 0.09, and 0.08%. The R² were 0.73, 0.81, 0.81, and 0.89 with the corresponding root mean square errors 0.17, 0.15, 0.12, and 0.09%, respectively, in cross validation. The R² were 0.62, 0.80, 0.81, and 0.87, respectively, with the root mean square errors 0.25, 0.31, 0.28, and 0.30% in external validation. These results indicate that the method of NIRS has relatively high accuracy in the prediction of rice fat content. The four calibration models established in the present study should be useful for nutrient quality improvement in rice breeding.     

Seed Coat Cracking of Soybean (Glycine max [L.] Merr.) After Soaking and Cooking

Seed coat cracking after soaking (SCAS) and after cooking (SCAC) are unfavorable traits associated with soybeans for food uses, such as cooked and seasoned beans (nimame) and fermented steamed beans (natto) because they cause an inferior appearance of the products and clogging of the production lines. The variation and causes of SCAS and SCAC among cultivars have not yet been clarified, but if they are determined genetically, genetic modification could be possible. Cultivars showed considerable variations in SCAS and SCAC. Significantly positive seasonal correlations of SCAS (Spearman's rank correlation coefficient, ρ = 0.518) and of SCAC (ρ = 0.681) were observed among recombinant inbred lines (RILs) derived from the cross between cultivars Nattoshoryu and Hyokeikuro 3. Quantitative trait locus (QTL) analyses and statistical analyses using generalized linear models showed that QTLs for SCAS (qSCAS1 , qSCAS2 , and qSCAS3 ) and SCAC (qSCAC1 and qSCAC2 ) were located on chromosomes 4 (linkage group [LG]: C1), 6 (LG: C2), and 8 (LG: A2) of the RILs. Interactions between QTLs were also observed. SCAS and SCAC are traits controlled by QTLs, which could provide significant insight into their causes and mechanisms. These undesirable characteristics could be improved through breeding.     

稻米蒸煮特性QTL定位及与感官食味品质的相关性分析

稻米蒸煮特性和感官食味品质是稻米品质的重要评价指标,其遗传复杂.为挖掘与利用优异的稻米品质基因,本研究利用籼稻昌恢121为受体亲本和优质粳稻越光为供体亲本构建的一套染色体片段置换系(CSSL),对稻米的吸水率(WA)、延伸率(CRE)和膨胀率(VE)3个蒸煮特性进行QTL定位.共检测到4个QTL,分布于第8和第11号染...     

外源铁蛋白基因对水稻重要性状表达的影响

以原始亲本"秀水11"为轮回亲本,Fer转基因高代系("Fer34")为非轮回亲本,采用连续回交和自交,结合GUS组织染色检测,获得了性状稳定、且带有外源Fer基因的"Fer34-XS11",它与原"秀水11"组成近等基因系。对该近等基因系的重要农艺性状、品质性状、抗病性状等进行考察。结果表明,外源Fer基因对水稻导入系无不良影响,转基因系基本保持了原亲本的生物学特性。     

REVIEW: Wild Rice: Both an Ancient Grain and a Whole Grain

Wild rice (Zizania spp.) grows in shallow waters of North America and is distinct from brown and white rice (Oryza spp.). The recent trends toward gluten‐free foods and ancient grains present an opportunity for increased interest in the health benefits of wild rice. Wild rice is classified as a whole grain and typically contains 75% carbohydrate, 6.2% dietary fiber, 14.7% protein, and 1.1% lipids. Wild rice is a good source of dietary fiber and has nearly double the amount of protein of white rice. The lipid content is low; however, most of the lipids are essential omega‐6 (35.0–37.8%) and omega‐3 (20.0–31.5%) fatty acids. In addition to macronutrient content, wild rice contains phytosterol levels several times higher than white rice. Furthermore, the antioxidant activity of wild rice is 10–15 times higher than white rice. A series of rat studies in which wild rice was added to a high fat, high cholesterol diet found significant attenuation of serum free fatty acids, total cholesterol, and triglyceride levels while maintaining higher high‐density lipoprotein levels compared with a control diet. The exact explanation of the protective mechanism of wild rice is uncertain, but the dietary fiber, phytosterol, or antioxidant capacity of wild rice may be the reason for it. Current interest in whole grains and gluten‐free diets, as well as antioxidants and phytochemicals, makes wild rice an attractive grain addition to the diet.     

水旱稻根基粗、千粒重主效QTL近等基因系的构建及鉴评

近等基因系的选育是分子遗传图谱构建、数量性状基因定位及分子标记辅助育种的重要基础之一。本文利用分子标记辅助目标性状QTL前景选择及恢复轮回亲本基因组的背景选择，再结合表型选择获得了定位在水稻4号、6号染色体上根基粗、千粒重2个主效QTL的近等基因系。其中有9个系入选旱田根基粗主效QTL brt4.1的近等基因系，根基粗的表型值为1.07～1.16mm，较轮回亲本越富提高6.11％～15.18％，平均遗传背景恢复率达97.22％；千粒重主效QTL的近等基因系有11个系入选，千粒重的表型值为21.25～26.25g，较轮回亲本越富的增幅为7.05％～32.16％，平均遗传背景恢复率为95.97％。另外，本文还就分子标记辅助近等基因系选育中背景选择标记数的确定、基于QTL-NILs的基因克隆等进行了讨论。     

水稻苗期不同阶段与低氮耐性相关的QTL分析

以超级杂交稻协优9308(协青早B/中恢9308)的重组自交系(R IL)为材料,通过溶液培养试验检测苗期不同阶段与低氮耐性相关的数量性状基因座(QTL)。结果共检测到14个QTLs,单个QTL可解释的表型变异为7.13%1~3.03%。其中,处理后15 d检测到6个QTLs,分别位于第1、7、1、7、10和11染色体上;处理后30 d检测到8个QTLs,分别位于第3、8、3、10、3、8、10和4染色体上。处理后15 d,在第1染色体RM297-RM212区间检测到同时控制相对冠干重和相对总干重的QTL,与氮循环有关,此染色体区域可能富含关键的氮代谢基因。定位结果表明,两个时间检测出的低氮耐性QTL的差异表达与水稻不同发育阶段基因的时空表达密切相关,从而反映在低氮耐性位点的差异上。     

Chemical Constituents,Dietary Fiber,and γ‐Oryzanol in Six Commercial Varieties of Brown Rice from Taiwan

In the interest of promoting the consumption of whole grains, the chemical constituents (moisture, protein, ash, and fat) and biofunctional components (dietary fiber and γ‐oryzanol) were determined in six varieties of brown rice (five japonica and one indica) that are preferred in the form of polished rice by consumers in Taiwan. The results showed significant differences (P < 0.05) in the chemical compositions of the samples for all the measured parameters. The Koshihikari variety had the highest contents of protein and crude ash. Crop year showed significant effects on the moisture content and partly on the protein, ash, and fat contents. The total dietary fiber content of the tested rice ranged between 5.1 and 10.0%, with Kaohsiung 145 having the highest content (P < 0.05). In all varieties, the content of insoluble dietary fiber was greater than that of soluble dietary fiber. The content (mg/100 g) of γ‐oryzanol ranged from 17.9 to 29.2 for the 2009 crop and from 24.5 to 41.3 for the 2010 crop. It showed that γ‐oryzanol was affected by crop year and variety. The japonica types had significantly higher γ‐oryzanol content (P < 0.05) than the indica type. Taikeng 9 and Tainan 11 had greater γ‐oryzanol content than the other rice varieties.     

A Novel Modified Endosperm Texture in a Mutant High‐Protein Digestibility/High‐Lysine Grain Sorghum (Sorghum bicolor (L.) Moench)

Development of high‐protein digestibility (HPD)/high‐lysine (hl) sorghum mutant germplasm with good grain quality (i.e., hard endosperm texture) has been a major research objective at Purdue University. Progress toward achieving this objective, however, has been slow due to challenges posed by a combination of genetic and environmental factors. In this article, we report on the identification of a sorghum grain phenotype with a unique modified endosperm texture that has near‐normal hardness and possesses superior nutritional quality traits of high digestibility and enhanced lysine content. These modified endosperm lines were identified among F₆ families developed from crosses between hard endosperm, normal nutritional quality sorghum lines, and improved HPD/hl sorghum mutant P721Q‐derived lines. A novel vitreous endosperm formation originated in the central portion of the kernel endosperm with opaque portions appearing both centrally and peripherally surrounding the vitreous portion. Kernels exhibiting modification showed a range of vitreous content from a slight interior section to one that filled out to the kernel periphery. Microstructure of the vitreous endosperm fraction was dramatically different from that of vitreous normal kernels in sorghum and in other cereals, in that polygonal starch granules were densely packed but without the typically associated continuous protein matrix. We speculate that, due to the lack of protein matrix, such vitreous endosperm may have more available starch for animal nutrition, and possibly have improved wet‐milling and dry‐grind ethanol processing properties. The new modified endosperm selections produce a range that approaches the density of the vitreous parent, and have lysine content and protein digestibility comparable to the HPD/hl opaque mutant parent.     

DETECTION AND VERIFICATION OF QUANTITATIVE TRAIT LOCI AFFECTING TOLERANCE TO LOW PHOSPHORUS IN RICE

Phosphorus (P)-deficiency in rice (Oryza sativa L.) may cause yields reductions. This research was conducted to map quantitative trait loci (QTL) for tolerance to low-P stress in a double-haploid (DH) line, and to verify these loci in another SSD9 population, which is the ninth generation of single-seed-distribution population derived from the same parents. Two populations were cultured solution at different period. By using the linkage map, QTLs for traits associated with tolerance to low-P stress were located. Results indicated that for DH population, one restricted fragment length polymorphism (RFLP) marker located on chromosome 6 was closely associated with relative root dry weight, relative shoot dry weight, and relative total dry weight. Two QTLs affected relative P uptake content. One micro-effect QTL was found to be associated with relative P utilization efficiency. For relative amounts of root exuded acid phosphatase, relative P allocation between shoot and root, relative plant P concentration, and relative shoot P concentration, one micro-effect QTL was detected for each one. Quantitative trait loci for 3 traits were detected for both DH and SSD9 populations, but the loci for each located trait were inconsistent between two populations; the reason for inconsistency in QTLs was analyzed. The main reason could be the difference in solution environment.     

Genetic Analysis of Kafirins and Their Phenotypic Correlations with Feed Quality Traits,In Vitro Digestibility,and Seed Weight in Grain Sorghum

Twenty‐three entries of grain sorghum (Sorghum bicolor (L.) Moench), including eight inbred lines (five males and three females) and 15 hybrids, were evaluated to determine the proportion of γ, αII, and β‐αI‐kafirins and their association with contents of crude protein, fat, and starch; protein digestibility; in vitro dry matter disappearance; and seed weight. The male lines included three normal‐seeded lines (TX2737, TX435, and P954063) and two large‐seeded lines (Eastin1 and PL‐1). Female lines consisted of three common U.S. seed parent lines (Wheatland, Redlan, and SA3042). The lines and their hybrids were grown under dryland conditions at two locations in Kansas using a randomized complete block design. The effects of genotype, location, and males were significant for all kafirins. Wide variations in composition and general combining ability (GCA) for kafirin content were noted among parent lines and hybrids, with TX2737, Eastin1, and PL1 having the largest GCA values for γ (1.37), αII (1.99), and β‐αI (2.57), respectively. Correlations among kafirins ranged from ‐0.89 to 0, whereas those of kafirins with feed quality traits, digestibility, and seed weight ranged from ‐0.45 to 0.48.