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 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.

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）

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.

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.

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.

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.

烟草生物碱性状的QTL定位

生物碱是烟草的重要化学成分。为明确烟草生物碱的遗传结构,发掘控制相关性状的主效位点,以烟草品种Y3、K326为亲本,构建大小为271的重组自交系群体。分别于2018、2019和2020年在云南省昆明市石林、玉溪市研和种植群体材料,检测总植物碱(TPA)、烟碱(NIC)、降烟碱(NOR)、假木贼碱(ANAB)和新烟草碱(ANAT)5种生物碱表型。对群体进行基因组测序,构建包含46,129个标记的遗传连锁图谱。利用基于混合线性模型的QTL定位方法及软件QTLNetwork2.0,进行QTL定位分析。共定位15个具有显著加性效应的QTL,加性效应对表型贡献率为0.58%~11.57%。其中4个主效QTL即控制总植物碱的qTPA14、烟碱的qNIC14、假木贼碱的qANAB14和新烟草碱的qANAT14,均可以解释相应性状10%以上的表型变异,且均位于14号连锁群上。6个QTL具有显著的加性与环境互作效应,对表型贡献率为0.80%~1.81%。5对QTL具有显著加性-加性上位性效应,对表型的贡献率为0.15%~2.31%。2对QTL具有显著的上位性与环境互作效应,对表型的贡献率为0.81%~1.16%。研究结果为进一步分离候选基因、解析遗传机理和促进烟草生物碱性状分子改良奠定了基础。

基于不同遗传群体的大豆分枝数QTL定位分析

分枝数是大豆重要的农艺性状,与大豆株型结构、产量潜力和适应性密切相关。为挖掘大豆分枝数稳定遗传位点,本研究以多分枝大豆Charleston和主茎型大豆东农594为亲本构建的148份重组自交系群体(RILs)和以主茎型大豆绥农14和多分枝野生大豆ZYD00006为亲本构建的213份染色体片段代换系(CSSLs)2个遗传群体为试验材料,采用ICIMapping软件中的完备区间作图法(inclusive composite interval mapping,ICIM)和Win-QTL-Cart 2.5软件中的复合区间作图法(composite interval mapping,CIM),对2018-2021年两个遗传群体的分枝数表型数据进行QTL分析,对QTL置信区间内的候选基因进行挖掘。共检测到17个与大豆分枝数性状相关的QTL位点,其中qBNA2_1和qBNK_1在不同年份和不同群体中稳定出现,分布在第8和9号染色体。根据基因注释等信息对两个QTL区间内的候选基因进行筛选,并通过qRT-PCR预测Glyma.08G053700、Glyma.08G068200、Glyma.08G082400和Glyma.09G167100为调控分枝数的候选基因。本研究结果有助于探明大豆分枝数形成的遗传机制,为大豆理想株型研究提供候选基因与材料支撑。

济麦44/济麦229重组自交系群体籽粒蛋白质含量QTL分析

小麦籽粒蛋白质含量与面团流变学特性及加工特性的关系密不可分。本研究在2020—2021年济南试验基地(E1)及2021—2022年济南试验基地(E2)和济阳试验基地(E3)三个环境下,以“济麦44×济麦229”构建的包含285个家系的重组自交系群体(F2∶6RILs)为材料,利用小麦55K SNP芯片构建高密度遗传连锁图谱,对籽粒蛋白质含量进行QTL分析。结果共筛选到2344个SNP标记用于构建遗传连锁图谱,图谱总长度3349.95 cM,平均标记密度为1.43 cM/标记。通过对籽粒蛋白质含量的QTL分析,共检测到18个籽粒蛋白质含量相关QTL,分布在1A、1B、2B、3D、4B、4D、5A、5B、5D、7A、7B共11条染色体上。Qpc.saas.4B-1在E1、E2和E3三个环境和BLUE(最佳线性无偏估计)值中均被稳定检测到,可以解释3.26%~23.79%的表型变异。Qpc.saas.4D和Qpc.saas.5A在两个环境和BLUE值中被检测到,分别解释2.42%~11.18%和2.48%~5.47%的表型变异,且Qpc.saas.4D与小麦矮秆基因Rht-D1b物理位置重合。本研究中检测到的QTL新位点Qpc.saas.4B-1、Qpc.saas.4D和Qpc.saas.5A是控制籽粒蛋白质含量的主效基因,具有高表型变异解释率。本研究结果可为小麦品质育种提供分子标记及理论参考。

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.

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.

籼粳RILs孕穗期耐冷性研究

以昆明小白谷和大理早籼杂交培育的孕穗期耐冷性重组近交系(RIL)为材料进行籼粳稻区水稻耐冷性研究。结果表明: (1)籼粳稻区株高、穗下节长、穗长和总粒数均呈数量性状的分布特征。(2)籼粳稻区一些性状间的相关性存在一定的差异,冷凉粳稻区株高与结实率等性状密切关性;相反高温粳稻区穗颈长与穗部4个性状达极显著或显著相关。 (3)遗传研究表明对低温和高温均敏感的穗颈长和结实率受主效基因控制,多数弱耐冷单株的耐热性相对较强。

利用重组自交系(RILs)群体进行质量—数量性状的遗传分析——遗传模型和小麦产量性状遗传

本文提出了利用 RIL s群体进行质量数量性状分析的 4个遗传模型及统计分析方法。其中 ,模型 、 、 、 分别表示性状受 1对主基因、 2对独立的主基因、 2对 AABB× aabb型连锁的主基因、 2对 AAbb× aa BB型连锁的主基因与微效基因共同控制。可估算出主基因的加性效应 (dma,dmb)、互作效应 (im)、遗传方差 (σ2m)和连锁图距 (R) ,以及微效基因的遗传方差 (σ2 )等参数。利用 2个RIL s群体对小麦 8个产量性状分析结果表明 ,不但不符合正态分布的性状都能在表现型水平上检测到主基因的存在 ,符合正态分布的性状也都能在表现型水平上检测到主基因的存在 ,所分析的性状均是由主基因和微效基因共同控制的 ;主基因配适的模型有模型 、模型 和模型 ,其中 ,模型 即 2对主基因相斥型连锁所占比例较大 ;在 2对主基因存在时 ,大都有主基因间的互作效应 ,其值一般小于加性效应 ;主基因对变异的贡献大于微效基因 ,平均为 5 8.2 %。

利用籼粳交RILs群体的水稻粒形QTLs定位

为了深入剖析水稻粒形性状的遗传调控机理,以典型籼稻品种七山占（Qishanzhan）和典型粳稻品种秋光（Akihikari）为亲本构建的重组自交系群体为材料,于2011-2013年分别对各株系的粒长、粒宽和粒厚3个粒形性状进行表型测定,并基于完备区间作图法（ICIM）进行粒形性状基因定位研究。试验结果表明：共检测到27个控制粒形性状的QTLs,包括3个粒长QTLs,11个粒宽QTLs和13个粒厚QTLs,它们分布于第1,2,3,4,5,11和12号染色体上,可分别解释14.45%-38.48%,28.98%-52.36%和38.77%-44.23%的表型变异;进一步分析发现,在第3,5和12号染色体上检测到的粒形性状QTL位点较多,且呈簇分布;此外,检测到q GL12a,q GL12b,q GW1,q GW5a,q GT11a和q GT12b等6个较新的QTLs位点,其中控制粒宽的q GW5a连续3年表达稳定,是一个重演性极好的QTL位点。以上结果将为水稻粒形性状的QTL克隆和遗传改良奠定基础。

基于主成分分析的苦荞麦重组自交系农艺性状综合评价

为筛选出综合性状优良的种质,为苦荞麦高产品种的选育推荐材料,对选取的58个具有高产潜质的重组自交系(RILs)及其双亲的10个主要农艺性状进行遗传变异分析、相关性分析、主成分分析和聚类分析。结果表明,58个RILs各性状的变异系数介于5.71%~31.55%,其中,产量、生育期和主茎分枝数的变异系数较大,粒宽和籽粒周长的变异系数较小。产量与籽粒面积、籽粒周长、株高和千粒重呈极显著(P<0.01)正相关,与粒长和粒宽呈显著(P<0.05)正相关,与生育期呈极显著负相关,产量与上述指标的相关系数绝对值从大到小依次为千粒重>株高>籽粒面积>生育期>籽粒周长>粒宽>粒长。主成分分析结果表明,前4个主成分的累计贡献率达86.987%,分别是粒形与产量因子(39.940%)、粒宽因子(24.478%)、株高因子(11.667%)、主茎分枝数与生育期因子(10.893%)。基于综合评价结果及RILs与亲本间的方差分析,共筛选出R64、R103、R164、R84、R192、R153和R214等7个综合性状优良的非米荞型RILs。这7个株系在聚类分析中均被划分在了高产、大粒、高秆和生育期短的C2类群,可将其作为示范推广品种或西南地区常规苦荞育种的优良种质资源加以利用。米荞型株系R52、R198和R101的产量极显著或显著高于米荞型亲本小米荞,可用于苦荞麦高产薄壳品种的选育。

02428×合系35 RILs群体糙米和发芽糙米γ-氨基丁酸、抗性淀粉的遗传分析

以水稻02428×合系35的RILs群体及其亲本糙米和发芽糙米为材料,对糙米、发芽糙米各222个群体样品的γ-氨基丁酸、抗性淀粉含量进行测定,以期选育出高γ-氨基丁酸、高抗性淀粉的水稻新品种。研究结果表明,重组自交系糙米、发芽糙米γ-氨基丁酸含量差异不大,群体间存在广泛变异,由主效基因控制。重组自交系糙米、发芽糙米抗性淀粉含量差异大,发芽糙米抗性淀粉平均含量是该群体糙米的1.2倍,群体间存在广泛变异,呈偏态分布。高海拔冷凉气候有利于糙米高抗性淀粉含量的提升与进化。本研究可以为功能水稻的遗传及品种选育提供一定的理论依据。