Low-Temperature Response to Major Agronomic Traits by Using Recombinant Inbred Line(RIL) Populations Derived from Towada × Kunmingxiaobaigu

Development of the recombinant inbred line populations （RILs） is important basis to detect QTLs for cold tolerance at booting stage in rice. A set of 230 RILs derived from the cross of Towada and Kunmingxiaobaigu were used for evaluation of low-temperature response on major agronomic traits of plant height （PH）, panicle length （PL）, panicle exsertion （PE）, spikelet fertility （SF）, specific spikelet fertility （SSF）, and spikelets per panicle （SPP） under natural low-temperature growing environments in Yunnan Province, China. The results showed PH, PE, and SPP were mainly attributed by genotypes. PL was mainly influenced interactively by the genotypes × environments. SF and SSF were mainly controlled by the environments. Under the five different growth environments, F values of the six agronomic traits mentioned above ranged from 4.019 to 97.284. Significant difference was revealed between the lines. Under every environment, it indicated significantly positive correlation between SF and SSF, with correlation coefficients ranged from 0.826 to 0.885. It indicated significantly positive correlation between PH, PL, and PE. Under five different growing environments, variation coefficients of the six characters ordered in SSF （66.3%） 〉 PE （57.4%） 〉 SP （37.2%） 〉 SPP （16.2%） 〉 PH （9.6%） 〉 PL （6.4%）. SSF, PE and SF were most sensitive to low temperature stress at booting stage, while SPP, PH and PL being least. The RILs of Towada/ Kunmingxiaobaigu can be used as a genetic population to investigate cold tolerance at booting stage. SSF, PE and SF are most sensitive to cold tolerance at booting stage in rice. So far the the variation of PH, PL, and SPP related to cold tolerance are not clear under natural low-temperature environment. More tested environments and years are required to identify and evaluate cold tolerance at booting stage in rice.

Combining Ability Analysis on Yield Traits of Recombinant Inbred Lines in Hybrid Rice

A population of 140 recombinant inbred lines at F8 generation were obtained after seven successive generations of self-pollination using single seed descent（SSD） method from the F2 hybrids of three-line restorers Luhui 8258 with high combining ability and Yanghui 34. Then, the 140 inbred lines obtained above and their parents Luhui 8258 and Yanghui 34 were crossed with three different types of cyto-plasmic male sterile（CMS） lines（Gang 46 A, Ⅱ-32 A and Lu 98A） according to NCⅡ design. The resulting 426 combinations were planted at Deyang and Suining bases to test the combining ability and inheritance of five yield traits： yield per plant, panicle number per plant, filled grain number per panicle, seed setting rate and 1 000-grain weight. The results showed that the variances of both general and specific combining abilities of the five traits all reached a significant or extremely significant level at the two sites. The broad and narrow heritability of the yield traits（except 1 000-grain weight whose broad and narrow heritability were both over70%） were all below 50% at the two experimental bases, suggesting that the four traits were easily subjected to environment influence. Very significant positive correlation of general combining ability was found between yield per plant and other traits except 1 000-grain weight. The general combining ability variance showed a normal distribution among the recombinant inbred lines at two sites, right in line with inheritance of quantitative traits. So, the genes controlling rice general combining ability can be targeted by QTL mapping.

Mapping of QTLs for Sheath Blight Resistance Using Recombinant Inbred Lines of Rice(Oryza sativa L.)

A recombinant inbred line （RIL） population composed of 157 lines derived from an inter-subspecific hybrid of Daguandao/IR28 by the single seed descent method was used as materials, and the quantitative trait loci （QTLs） coffering the resistance to sheath blight in the 157 RILs and the parents were detected using the toothpick inoculation method. The disease indexes of rice sheath blight in the two parents and 157 RILs were scored and the QTLs responsible for rice sheath blight resistance were detected accordingly by QTL Cartographer software. The results showed that a total of 4 QTLs （qsbl, qsb2, qsb5-1, qsb5-2） conferring sheath blight resistance were detected on chromosomes 1, 2 and 5, and their variance explained ranged from 10.41% to 36.92%. The additive effect of qsb5-1 was negative, indicat- ing that the QTLs derived from donor parent IR 28 could enhance the resistance to sheath blight. However, the additive effects of qsbl, qsb2 and qsb5-2 were positive, indicating that the QTLs derived from donor parent Daguandao weakened the resis- tance to sheath blight.

Genetic analysis and QTL mapping of stalk cell wall components and digestibility in maize recombinant inbred lines from B73 × By804

The cell wall composition and structure of the maize stalk directly affects its digestibility and in turn its feed value.Previous studies of stem quality have focused mostly on common maize germplasm,and few studies have focused on high-oil cultivars with high grain and straw quality.Investigation of the genetic basis of cell wall composition and digestibility of maize stalk using high-oil maize is desirable for improving maize forage quality.In the present study,a high-oil inbred line(By804)was crossed as male parent with the maize inbred line B73 to construct a population of 188 recombinant inbred lines(RILs).The phenotypes of six cell-wall-related traits were recorded,and QTL analysis was performed with a genetic map constructed with SNP markers.All traits were significantly correlated with one another and showed high broad-sense heritability.Of 20 QTLs mapped,the QTL associated with each trait explained 10.0%–41.1%of phenotypic variation.Approximately half of the QTL each explained over 10%of the phenotypic variation.These results provide a theoretical basis for improving maize forage quality by marker-assisted selection.

Identification of Stable Quantitative Trait Loci for Sheath Blight Resistance Using Recombinant Inbred Line

To identify stable quantitative trait loci(QTLs)responsible for sheath blight resistance,a recombinant inbred line mapping population consisting of 219 lines was developed by crossing Lemont and Yangdao 4.Average disease rating,average lesion length,maximum disease rating and maximum lesion length were assayed in six different environments.A total of 128 minor effect QTLs were detected by multiple interval mapping.These QTLs explained less than 11.2%of the phenotypic variations individually,and 106 QTLs were clustered in 20 QTL-rich regions/putative loci.Significant QTL×environment interactions were detected at three putative loci(qSBR11.1,qSBR11.2 and qSBR11.3),indicating that these three loci were not stable.The other 17 stable loci(qSBR1.1,qSBR1.2,qSBR2.1,qSBR2.3,qSBR3.1,qSBR3.2,qSBR3.5,qSBR3.6,qSBR5.1,qSBR7.1,qSBR8.1,qSBR9.1,qSBR9.2,qSBR9.3,qSBR12.1,qSBR12.2 and qSBR12.4)provided a foundation for marker-assisted selection in breeding.Analysis of allelic effect on the 20 putative loci identified 7 highly stable loci,including qSBR3.2,qSBR7.1,qSBR8.1,qSBR9.2,qSBR9.3,qSBR12.1 and qSBR12.2.

Diversity, Structure, and Marker-Trait Association Analysis of the Maize Recombinant Inbred Line Population

Association mapping has emerged as a new tool to elucidate complex quantitative trait loci in maize, but there are few reports about systematic association analysis for the specific SSR markers with agronomic traits of interest in China. We investigated the morphological and genetic diversity and population structure for 76 maize recombinant inbred lines, and then association analysis were further performed between 48 simple sequence repeat loci and 17 morphological traits, consisting of nine ear-related traits and eight other traits. The 48 SSR markers were screened out and further classified into two groups including a group of loci in regions harboring reported quantitative trait loci that affect ear shape and a group of markers distributing on the whole genome randomly. The result indicated that the population of recombinant inbred lines was structured, showing five subpopulations. Our association results revealed that there were 82, 59, and 40 significant associations detected by K-test, logistic regression, and both analysis, respectively. When the 17 traits were considered separately, the significant associations between Q-SSRs and E-traits were raised to 27.8%, whereas the other groups of combinations ranged between 2.3 and 6.3%. As the proportion of significant associations is higher among the Q-SSR subset of markers and the subset of traits related to ear shape than those for all of the other combinations, we conclude that this approach is valid for establishing true positive marker-trait relationships. Our results also demonstrated that association mapping could complement and enhance previous QTL information for marker-assisted selection.

Identification of QTLs for Blast, Bacterial Blight, and Planthopper Resistance Using SNP-Based Linkage Maps from Two Recombinant Inbred Rice Lines

Rice is the most significant global food security. Several biotic factors limit rice production, breeding biotic-resistant rice has, therefore, become an increasingly important goal. Two elite rice lines, IR71033-121-15 (IR71033) and IR57514-PMI-5-B-1-2 (IR57514), provide potential genes for biotic stress resistance traits. In this study, genotyping by sequencing (GBS) for single nucleotide polymorphism (SNP)-based linkage map construction was used to detect quantitative trait loci (QTLs) for blast (BL), bacterial blight (BB), whitebacked planthopper (WBPH), and brown planthopper (BPH) resistance. IR71033 was derived from Oryza minuta and carried BL, BB, WBPH, and BPH resistance QTLs. IR57514 is a well-adapted rainfed lowland line that carries BL and BB resistance QTLs. Two sets of recombinant inbred line (RIL) populations derived from crosses of KDML105 × IR71033 and KDML105 × IR57514 were used to dissect the genetic basis of disease and insect pest resistance. The RIL populations were evaluated for BL, BB, WBPH, and BPH resistance from 2016 to 2018 at four rice research centers in Thailand. From these, we identified a large number of SNPs through GBS and constructed high-resolution linkage maps. By combining phenotypic evaluation with the GBS data, a total of 24 QTLs on four chromosomes were detected that confered pest resistance and explained 7.3% - 61.4% of the phenotypic variance. These findings should facilitate identifying novel resistance genes and applying marker-assisted selection for resistance to the four major rice pests investigated here. These strategies will improve the resilience and reliability of rice varieties adapted to the low-yielding environment of rainfed lowland areas worldwide.

Identifying Genomic Regions Conferring Morphological and Yield-related Traits in Soybean Based On A Four-way Recombinant Inbred Line Population

Improvement of seed yield of soybean(Glycine max(L.)Merr.)is generally achieved by combining morphological and yield-related traits,such as plant height(PH),node number on main stem(NN),pod number per plant(NP),seed number per plant(NS),100-seed weight(HSW)and seed weight per plant(SWPP).Identifying quantitative trait loci(QTLs)for morphological and yield-related traits is therefore important for breeding.In this study,a four-way recombinant inbred line population comprising 160 lines derived from the cross(Kenfeng14×Kenfeng15)×(Heinong48×Kenfeng19)was planted in five different environments and morphological and yield-related trait data were used to identify QTLs by the inclusive composite interval mapping method.Totally 38 QTLs for PH,40 QTLs for NN,26 QTLs for NP,10 QTLs for NS,26 QTLs for HSW and 49 QTLs for SWPP were detected in 125 genomic regions.Single QTLs explained 2.17%-14.60%,2.00%-10.04%,2.37%-9.77%,2.62%-8.61%,0.47%-6.51%and 0.14%-12.39%of the phenotypic variation for PH,NN,NP,NS,HSW and SWPP,respectively.Among these 125 genomic regions,120 were newly associated with morphological and yield-related traits.The results would facilitate the molecular breeding of morphological and yield-related traits in soybean.

Genetic analysis and QTL mapping of growth period traits and plant height traits in soybean recombinant inbred lines from Dongnong 47 × PI 317334-B

High and stable yield is the main goal of soybean genetic improvement.In this study,association analysis was used to detect the quantitative trait loci(QTL)for the plant height,and soybean growth period using 182 SSR markers in the RIL population of 136 F_(4:8) lines,which developed from a cross between photoperiod-insensitive cultivar‘Dongnong 47’and photoperiod-sensitive variety PI317334–B.The results showed that 33 QTLs related to soybean growth period and plant height traits were detected by compound interval mapping,and were located on 12 linkage groups including N,C1,C2,J,D1a,B2,E,G,A2,O,L,I,with the contribution rate of 7.85–33.84%.These QTL loci and linkage markers related to soybean photoperiod sensitivity,would be helpful to identify key genes that control soybean photoperiod sensitivity,and provide an important basis for the breeding of new photoperiod-insensitive soybean varieties based on molecular design breeding.

QTL mapping of grain appearance quality traits and grain weight using a recombinant inbred population in rice(Oryza sativa L.)

supported by a grant from the National High-Tech R＆D Program of China （2014AA10A603, 2014AA10A604）;a grant from the Youth Foundation in Sichuan, China （2011JTD0022）;the special fund for China Agricultural Research System （CARS-01-08）;the Provincial Specialized Funds for Innovation Ability Promotion in Sichuan, China （2013GXJS005）

甘蓝型油菜RIL群体苗期根系耐铝性鉴定及评价方法研究

为减少铵肥的大量施用以及酸雨频降引发的耕地酸化,从而影响作物的生长,利用综合评价方法通过幼苗期根系表型筛选耐铝种质.以甘蓝型油菜重组自交系(RIL)亲本10D130和中双11为材料筛选苗期适宜的铝胁迫浓度,使用该浓度处理RIL内138个品种(系)幼苗,对其根长、根表面积、根平均直径、根体积、根交叉数、根尖数和根干质量7个根系指标的铝毒单项耐性系数进行变异系数分析、相关性分析、主成分分析、系统聚类分析和逐步回归分析,并采用隶属函数法综合评价不同油菜品种(系)根系的耐铝特性.结果表明:138份油菜品种(系)间各项根系指标差异有统计学意义(p<0.05);筛选出甘蓝型油菜幼苗期耐铝毒品种(系)27034,27036和27007等.根据灰色关联度及逐步回归分析结果,认为根据根长、根表面积、根体积、根交叉数等7个关键指标,可以初步判断甘蓝型油菜种质幼苗期的耐铝毒特性.通过这些方法综合评价油菜对铝的耐受性,可以避免单一指标的片面性和不稳定性,结果更为可靠.

Mapping and Comparative Analysis of QTL for Rice Plant Height Based on Different Sample Sizes within a Single Line in RIL Population

To clarify the most appropriate sample size for obtaining phenotypic data for a single line,we investigated the main-effect QTL(M-QTL) of a quantitative trait plant height(ph) in a recombinant inbred line(RIL) population of rice(derived from the cross between Xieqingzao B and Zhonghui 9308) using five individual plants in 2006 and 2009.Twenty-six ph phenotypic datasets from the completely random combinations of 2,3,4,and 5 plants in a single line,and five ph phenotypic datasets from five individual plants were used to detect the QTLs.Fifteen M-QTLs were detected by 1 to 31 datasets.Of these,qph7a was detected repeatedly by all the 31 ph datasets in 2006 and explained 11.67% to 23.93% of phenotypic variation;qph3 was detected repeatedly by all the 31 datasets and explained 5.21% to 7.93% and 11.51% to 24.46% of phenotypic variance in 2006 and 2009,respectively.The results indicate that the M-QTL for a quantitative trait could be detected repeatedly by the phenotypic values from 5 individual plants and 26 sets of completely random combinations of phenotypic data within a single line in an RIL population under different environments.The sample size for a single line of the RIL population did not affect the efficiency for identification of stably expressed M-QTLs.

Mapping Quantitative Trait Loci Associated with Aluminum Toxin Tolerance in NJRIKY Recombinant Inbred Line Population of Soybean (Glycine max)

To investigate the genetic mechanism of AI-tolerance in soybean, a recombinant inbred line population （RIL） with 184 F2：7：11 lines derived from the cross of Kefen9 No.1×Nannong 1138-2 （AI-tolerant×AI-sensitive） were tested in pot experiment with sand culture medium in net room in Nanjing. Four traits, i.e. plant height, number of leaves, shoot dry weight and root dry weight at seedling stage, were evaluated and used to calculate the average membership index （FAi） as the indicator of AI-tolerance. The composite interval mapping （CIM） under WinQTL Cartographer v. 2.5 detected five QTLs （i.e. qFAi-1, qFAi- 2, qFAi-3, qFAi-4 and qFAi-5）, explaining 5.20%-9.07% of the total phenotypic variation individually. While with the multiple interval mapping （MIM） of the same software, five QTLs （qFAi-1, qFAi.5, qFAi.6, qFAi-7, and qFAi-8） explaining 5.7%-24.60% of the total phenotypic variation individually were mapped. Here qFAi-1 and qFAi-5 were detected by both CIM and MIM with the locations in a same flanking marker region, GMKF046-GMKF080 on B1 and satt278-sat_95 on L, respectively. While qFAi-2 under CIM and qFAi-6 under MIM both on Dlb2 were located in neighboring regions with their confidence intervals overlapped and might be the same locus. Segregation analysis under major gene plus polygene inheritance model showed that AI-tolerance was controlled by two major genes （h^2mg=33.05%） plus polygenes （h^2pg=52.73%）. Both QTL mapping and segregation analysis confirmed two QTLs responsible for AI-tolerance with relatively low heritability, and there might be a third QTL, confounded with the polygenes in segregation analysis.

Quantitative trait locus analysis of lateral branch-related traits in cucumber(Cucumis sativus L.)using recombinant inbred lines

A group of 224 recombinant inbred lines (RILs) was derived from a narrow cross between 2 cucumber (Cucumis sativus L.) lines, namely, S94 (Northern China type with weak lateral branch growth potential and early lateral branch sprouting time) and S06 (Northern European type with strong lateral branch growth potential and late lateral branch sprouting time). These lines were then used for investigating lateral branch-related traits. A total of 36 quantitative trait loci (QTLs) were detected for the following 4 lateral branch-related traits: lateral branch average length (LBAL), lateral branch total length (LBTL), lateral branch number (LBN), and first lateral branch node (FLBN). Further, each QTL explained 3.1% (lbtl2.1, spring) to 32.3% (lbn2.3, spring) of the observed phenotypic variance. Eleven QTLs (lbal1.1, lbtl1.1, lbn1.2, flbn1.2, etc.) for different traits were found to be clustered on the e23m18d-ME23EM6c section (7.4 cM) of linkage group (LG) 1; further, 15 QTLs (lbal2.1, lbtl2.1, lbn2.1, flbn2.1, etc.) were found to be clustered on the S94A1-ME4SA4a section (13.9 cM) of LG2. Twenty-one QTLs explained more than 10% of the phenotypic variance. Moreover, lbtl1.3 (autumn, 26.2%, logarithm of odds (LOD) = 17.4; spring, 26.9%, LOD = 17.9) had stable position and contribution in both seasons. Several se-quence-anchor markers (CMBR40, F, CS30, S94A1, CSWTA11B, etc.) were closely linked with some QTLs for LBAL, LBTL, LBN, and FLBN, which can be used for the marker-assisted selection to improve the plant architecture in cucumber breeding.

利用RIL群体分析小麦淀粉粘度性状与馒头品质的关系

利用重组自交系群体对淀粉粘度性状与馒头品质间的关系进行了全面分析。相关分析表明,峰值粘 度、低谷粘度、最终粘度、反弹值、峰值时间均与馒头外观、结构、弹韧性、粘性、总分等5项指标呈显著正相关;回归分 析结果表明,粘度性状与馒头品质间存在较强的线性关系,建立了馒头体积、比容、结构、弹韧性、粘性和总分与淀粉 粘度性状的回归方程;通过通径分析明确了各粘度性状对馒头品质的直接效应和间接效应。

QTL Mapping of Yield and Yield Components for Elite Hybrid Derived-RILs in Upland Cotton

A population of 180 recombinant inbred lines （RILs） was developed by single seed descended from the cross of high yield Upland cotton （Gossypium hirsutum L.） varieties Zhongmiansuo12 （ZMSI2） and 8891, the two parents of Xiangzamian2 （XZM2）. A genetic linkage map consisting of 132 loci and covering 865.20 cM was constructed using the RIL population chiefly with SSR markers. Yield and yield components were investigated for RILs in three environments in China. The purpose of the present research was to analyze the relationship between yield and its components and to map QTL for yield and yield components in cotton. QTL were tagged with data sets from single environment （separate analysis） and a set of data from means of the three environments （joint analysis）. A total of 34 QTL for yield and yield components were independently detected in three environments, whereas fifteen QTL were found in joint analysis. Notably, a stable lint percentage QTL qLP-A10-1 was detected both in joint analysis and in two environments of separate analysis, which might be of special value for marker-assisted selection. The QTL detected in the present study provide new information on improving yield and yield components. Results of path analysis showed that bolls/plant had the largest contribution to lint yield, which is consistent with the mid-parent heterosis value in F1. Accordingly, in cotton breeding, bolls/plant can be considered first and other yield components measured as a whole to implement variety enhancement and hybrid selection of cotton.

利用RIL群体进行小麦品质性状及其与产量性状的相关分析

利用小麦重组自交系(RIL)群体,对小麦主要品质性状、及其与产量的关系进行了分析。结果表明,RIL群体品质、产量性状都表现了较大的变异幅度;蛋白质各性状内、淀粉各性状内相关性多数显著,但二者之间相关性多不显著,这说明在小麦品种改良中,优良的蛋白质性状和优良的淀粉性状可以兼得;稳定时间、沉降值等重要的加工品质性状和淀粉性状与产量相关不显著,说明加工品质可以与产量很好地协调起来;适当降低千粒重,增加穗数,有利于强筋的形成和粘度的提高;矮杆、半矮杆性状能够与良好的加工品质、高蛋白质含量、高GMP含量协调起来。

利用RIL群体分析小麦品质与中国干面条加工品质的关系

为了解小麦品质对面条品质的影响,以RIL群体为材料,对小麦品质性状与面条品质间的关系进行了全面的分析。简单相关分析表明,面团形成时间和稳定时间与面条品质指标呈显著正相关,除了峰值粘度与胶凝值外,其它的RVA参数均与面条的光滑度呈显著相关。但蛋白质含量、GMP含量、湿面筋含量、干面筋含量、沉淀值、直链淀粉含量、支链淀粉含量、降落值、膨胀势、峰值粘度等多数性状与面条品质相关均不显著。回归分析结果表明,影响面条品质的小麦品质性状主要有蛋白质含量、GMP含量、沉淀值、面团形成时间、稳定时间和稀懈值,并建立了面条品质与以上性状的回归方程。通过通径分析明确了蛋白质含量、面团形成时间、稳定时间以及稀懈值对面条品质的作用主要以直接作用为主,GMP含量和沉淀值通过直接效应和间接效应的共同作用来影响面条品质。面团稳定时间是衡量面条加工品质的最重要的性状。

籼粳交DH群体和RIL群体的构建及籼粳分化

对籼粳杂交组合“0 2 42 8(粳 ) /特青 (籼 )”F1 进行一步成苗法花药培养 ,对该组合的分离世代采用连续自交随机选择 ,分别获得由 132个株系组成的加倍单倍体 (DH)群体和由 15 7个株系组成的重组自交系 (RIL )群体。通过形态指数法和分子标记法对两个群体的籼粳分化进行了研究 ,结果表明 ,无论是 DH群体还是 RIL群体 ,各株系的籼粳形态指数和分子标记指数分布均呈正态分布 ,但 RIL群体的偏态性强于 DH群体 。

水稻长穗大粒RIL群体产量、穗部和谷粒性状的遗传分析

为探讨水稻长穗大粒特异种质产量相关性状的遗传机制,以自育的一个水稻长穗、大粒品系FJCD与偏籼型三系恢复系密阳46通过杂交和单粒传法构建的含有130个品系的重组自交系群体(RILs)F9代为材料,采用植物数量性状的主基因+多基因混合遗传模型及其相应的统计方法,对水稻18个产量、穗部和谷粒性状进行遗传分析.结果表明,谷粒厚和谷粒宽厚比2个性状符合多基因遗传,无主基因存在,千粒重性状符合1对主基因+多基因遗传,谷粒宽性状符合3对主基因+多基因遗传,其他14个性状均符合2对主基因+多基因遗传.以主基因遗传率为主的性状包括单株谷重、结实率、每丛有效穗数、穗长、一次枝梗数、一次枝梗总长、二次枝梗总长、谷粒长宽比、谷粒宽;以多基因遗传率为主的性状包括谷粒长和谷粒长厚比.其中,千粒重和谷粒宽2个性状可能含有效应较大的主效QTL.