Genomics-assisted breeding——A revolutionary strategy for crop improvement

Food shortages arise more frequently owing to unpredictable crop yield losses caused by biotic and abiotic stresses. With advances in molecular biology and marker technology, a new era of molecular breeding has emerged that has greatly accelerated the pace of plant breeding. High-throughput genotyping technology and phenotyping platforms have enabled large-scale marker-trait association analysis, such as genome-wide association studies, to precisely dissect the genetic architecture of plant traits. Large-scale mapping of agronomically important quantitative trait loci, gene cloning and characterization, mining of elite alleles/haplotypes, exploitation of natural variations, and genomic selection have paved the way towards genomics-assisted breeding（GAB）. With the availability of more and more informative genomic datasets, GAB would become a promising technique to expedite the breeding cycle for crop improvement.

Development and application of marker-assisted reverse breeding using hybrid maize germplasm

Humankind has been through different periods of agricultural improvement aiming at enhancing our food supply and the performance of food crops. In recent years, whole genome sequencing and deep understanding of genetic and epigenetic mechanisms have facilitated new plant breeding approaches to meet the challenge of growing population, dwindling resources, and changing climate. Here we proposed a simple and fast molecular breeding method, marker-assisted reverse breeding（MARB）, which will revert any maize hybrid into inbred lines with any level of required similarity to its original parent lines. Since all the pericarp DNA of a hybrid is from the maternal parent, whereas one half of the embryo DNA is from the maternal parent and the other half from the paternal parent, so we firstly extract DNA from seed embryo and pericarp of a selected elite hybrid separately and then we derived the genotypes of the two parents with high-density single nucleotide polymorphism（SNP） chips. The following marker-assisted selection was performed based on an Illumina low-density SNP chip designed with 192 SNPs polymorphic between the two parental genotypes, which were uniformly distributed on 10 maize chromosomes. This method has the advantages of fast speed, fixed heterotic mode, and quick recovery of beneficial parental genotypes compared to traditional pedigree breeding using elite hybrids. Meanwhile, MARB has the advantage of not requiring sophisticated transformation and double haploid（DH） technologies over RNA interference（RNAi）-mediated reverse breeding. In addition, MARB can also be used with feed corn harvested from big farms, which is often similar to F_2 populations, and the relevant transgenes in the population can be eliminated by marker-assisted selection. As a result, the whole global commercial maize hybrids can be utilized as germplasm for breeding with MARB technology. Starting with an F_2 population derived from an elite hybrid, our experiment indicates that with three cycles of marker-assisted selection, selected lines could recover over 80% of the parental genotypes and associated beneficial genes in a fixed heterotic mode. The success application of MARB in maize suggests that this technology is applicable to any hybrid crop to breed new inbreds with improved hybrid performance but the same heterotic mode. As chip technology becomes cheap, it would be expected that polymorphism screening and following marker-assisted selection could be done with one all-purpose high density chip. Several issues associated with MARB were discussed, including its rationale, efficiency and advantages, along with food/feed and environmental safety issues and applications of MARB in variety protection and marker-assisted plant breeding.

Breeding Rice Restorer Lines with High Resistance to Bacterial Blight by Using Molecular Marker-Assisted Selection

Two bacterial blight （BB） resistance genes, Xa21 and Xa4, from IRBB24 were introduced into hybrid rice restorer line Mianhui 725, which is highly susceptible to BB, by using hybridization and molecular marker-assisted selection technology. Four homologous restorer lines were obtained through testing the R target genes with molecular markers and analyzing parental genetic background. Inoculation of the four lines and their hybrids with the specific strains of Xanthomonas oryzae pv. oryzae, P1, P6 and seven representative strains of Chinese pathotype, C Ⅰ -CⅦ, showed that all of the four lines and their hybrids were highly resistant and presented broad resistance-spectrum to BB. The hybrids of G46A / R207-2 displayed good agronomic characters and high yield potential, and R207-2 was named Shuhui 207.

Pyramiding Breeding by Marker-Assisted Recurrent Selection in Upland Cotton: Selected Effects on Resistance to Helicoverpa armigera

The coincidence rates were more than 96% among the instar-weighted average of bioassaysin the lab, the percentage of resistance to Km in the field and the percentage of plantscontaining Bt gene. So, the performance of resistance to Km in the field can be used torepresent the transgenic Bt gene for selecting the resistance to bollworm. The instar-weighted averages were 30.585, 24.182, 16.615, 10.601, 10.123, 7.440 and 7.215 for theC0, P1, M1, M2, MP1, P2 and MP2 populations, respectively. The variance analysisindicated that the instar-weighted average in C0 was greatly significantly higher thanthat in all other populations, i.e., the performance of resistance to bollworm in C0 washighly significantly lower than all other populations. And the resistance in P1 wasgreatly lower than that of M1, M2, MP1, P2 and MP2, and M1 greatly lower than that of M2,MP1, P2 and MP2. There were no significant differences among M2, MP1, P2 and MP2. Withinthe populations of the first cycle selection, MP1 and M1 were greatly significantlyhigher than P1, and MP1 significantly higher than M1. The populations of the second cycleselection were significantly higher than their initial population M1, but no significantdifference among them. The boll size, seed index, the percent of the first harvest yield,fiber length, strength and elongation of the resistant plants to bollworm were significantlylower than that of sensitive plants to bollworm. And the yield of seed and lint cottonof the resistant plant to bollworm were lower than that of the sensitive to bollworm, butno significant difference between them. The boll numbers per plant, lint percent andmicronaire of the resistant plants to bollworm were significantly higher than that of thesensitive plant to bollworm.

Microarray-assisted Marker Development for Molecular Breeding

The advantage of being able to investigate the abundance and composition of millions of sequences in parallel has established microarrays as an attractive technology for genome wide transcription and sequence variation pro-

Breeding of R8012,a Rice Restorer Line Resistant to Blast and Bacterial Blight Through Marker-Assisted Selection

Genetic improvement is one of the most effective strategies to prevent rice from blast and bacterial blight （BB） diseases, the two most prevalent diseases jeopardizing rice production. Rice hybrids with dural resistance to blast and BB are needed for sustainable production of food. An incomplete diallele design resulted in 25 crosses between five blast and five BB resistant germplasm accessions. Only one pair of parents, DH146 ×TM487, showed polymorphism for all the markers to identify one blast resistance gene Pi25 and three BB resistance genes, Xa21, xa13 and xa5, thus it was used in the marker-assisted selection （MAS）. F2 individuals of DH146× TM487 were genotyped using flanking markers of RM3330 and sequence tagged site （STS） marker SA7 for Pi25. The resistant F2 plants with Pi25 were used for pyramiding BB resistance genes Xa21, xa13 and xa5 identified by the markers pTA248, RM264 and RM153, respectively in subsequent generations. Finally, after selection for agronomic traits and restoration ability among 12 pyramided lines, we acquired an elite restorer line, R8012 including all four target genes （Pi25＋Xa21＋xa13＋xa5）. Hybrid Zhong 9NR8012 derived from the selected line showed stronger resistance to blast and BB, and higher grain yield than the commercial checks uniformally in experimental plots, 2007 state-wide yield trial and 2008 nation-wide yield trial. This study provides a paradigmatic example to show that MAS is a practically feasible tool in effectively pyramiding multiple resistance genes. The resultant restoring line and its hybrid would play an important role in securing rice production in China.

SCAR Markers Assisted Selection for a Bentazon Susceptible Lethality Gene (ben) in Rice

In progenies resulting from crosses involving rice cultivar Norin 8m susceptible to bentazon as the donor of ben gene, SCARs tightly linked to ben were utilized for selection of ben. The homozygous and heterozygous genotypes with ben could be identified with the SCARs. The molecular markers offer a powerful tool for indirect selection of ben and can accelerate the introgression of ben into current rice cultivars.

Marker-assisted pyramiding of soybean resistance genes R_(SC4),R_(SC8),and R_(SC14Q) to soybean mosaic virus

Soybean mosaic virus （SMV） is one of the major viral pathogens affecting soybean crops worldwide. Three SMV resistance genes, Rsc4, Rsc8, and Rsc14Q, have been identified and mapped on soybean chromosomes 14, 2, and 13 from Dabaima, Kefeng 1, and Qihuang 1 cultivars, respectively. Soybean cultivar Nannong 1138-2 is widely grown in the Yangtze River Valley of China. In this study, crosses were made between Qihuang l^Kefeng 1 and DabaimaxNannong 1138-2. Ten simple sequence repeat （SSR） markers linked to three resistance loci （Rsc4, Rsc8, and Rsc^4Q） were used to assist pyramided breeding. Pyramided families containing three resistance loci （Rsc4, Rsc8, and Rsc14Q） were evaluated by inoculating them with 21 SMV strains from China. Results indicated that the 10 markers can be used effectively to assist the selection of resistant individuals containing Rsc4, Rsc8, and Rsc14Q. A total of 53 F6 plants were confirmed to contain three homozygous alleles conferring resistance to SMV. Five F7 homozygous pyramided families exhibited resistance to 21 strains of SMV and showed desirable agronomic traits using dual selection. The strategy of pyramiding resistance gene derived from different varieties has practical breeding value in providing broad-spectrum resistance against the existing strains of SMV in China.

Improving Blast Resistance of a Thermo-Sensitive Genic Male Sterile Rice Line GD-8S by Molecular Marker-Assisted Selection

The broad-spectrum blast resistance gene Pi-1, from donor line BL122, was introduced into a thermo-sensitive genic male sterile rice line GD-8S, which possessed good grain quality but high susceptibility to rice blast, by using backcross breeding and molecular marker-assisted selection. Five elite improved male sterile lines, RGD8S-1, RGD8S-2, RGD8S-3, RGD8S-4 and RGD8S-5, were selected based on the results of molecular marker analysis, spikelet sterility, recovery rate of genetic background and agronomic traits. Thirty-three representative blast isolates collected from Guangdong Province, China were used to inoculate the improved lines and the original line GD-8S artificially. The resistance frequencies of the improved lines ranged from 76.47% to 100%, much higher than that of the original line GD-8S （9.09%）. On the agronomic characters, there were no significant differences between the improved lines and GD-8S except for flag leaf length and panicle number per plant. The improved lines could be used for breeding hybrid rice with high blast resistance.

Introgression of Drought Tolerance into Elite Basmati Rice Variety through Marker-Assisted Backcrossing

Drought is one of the major abiotic threat to rice production in the context of climate change.Super Basmati is an elite,fine grain basmati rice variety grown in Punjab,Pakistan.Due to drought sensitive in nature,its yield has been facing an alarming situation in production because of gradual decrease in irrigated water for a couple of years.Three reported novel QTLs for drought tolerance were selected for incorporation into Super Basmati by employing marker assisted selection strategy.IR55419-04 with novel QTLs was used as a donor parent.Foreground selection was performed by applying PCR based QTL linked SSR markers followed by recombinant selection by using 2-4 flanking markers.Background selection was exercised by using polymorphic SSR markers for maximum genome recovery of the Super Basmati.The individuals homozygous at the target QTLs and with maximum background of Super Basmati at the rest of the non-target genome was selected for evaluation of drought tolerance.Under drought stress conditions,the yields of all introgressed lines(ILs)were 44.2%-125.7%higher than recurrent parent.Six superior ILs that are drought tolerant and very similar to Super Basmati in terms of agronomic and grain quality traits are marked for release as drought-tolerant varieties in arid regions or for use in breeding programs of high grain quality and drought-tolerant parents.

性别特异分子标记在斑鳢全雄育种上的应用

为了快速筛选培育出全雄斑鳢,本研究结合性别特异分子标记和三系配套育种技术,开发了全雄斑鳢的育种方法。将健康的七日龄斑鳢幼鱼随机分成3组进行雌化处理,在饲料中分别添加雌二醇(E2)100、300、600 mg/kg,饲养60 d。利用性别特异分子标记引物M12、P2鉴定筛选出决定型为XY型斑鳢,将XY型正常雄鱼与XY型伪雌鱼交配,获得的子代分为两组,一组为投喂正常饲料,另一组进行雌激素投喂,利用MX1和MX3引物筛选出YY超雄鱼,最后将YY超雄鱼和正常雌鱼作为亲本交配生产出全雄斑鳢子代。结果显示,600 mg/kg激素浓度组的性逆转率最高,达75%,从508尾经雌激素E2投喂的家系中筛选获得235尾具有XY基因型斑鳢。XY伪雌鱼与正常雄鱼交配获得的子代在2月龄时检测到22尾YY超雄鱼,7月龄时检测到14尾YY超雄鱼,筛选获得YY超雄鱼个体用于生产全雄子代。本研究方法显著提高了全雄化斑鳢育种效率,缩短了育种周期,展现出巨大的经济潜力和应用价值,为其他鱼类开展性别特别分子标记辅助育种提供借鉴或参考。

抗稻瘟病水稻恢复系的分子标记辅助选育及抗性鉴定

【目的】开展抗稻瘟病水稻恢复系的分子标记辅助选育及抗性鉴定,为育成持久、广谱抗病优质杂交水稻新品种提供优异的遗传资源和技术参考。【方法】利用分子标记辅助选择和回交育种技术,将持久、广谱的抗稻瘟病基因Pi1、Pi2和Pigm导入恢复系桂R1703,获得了单基因、双基因和三基因导入系,并对其进行稻瘟病鉴定和农艺性状调查,分析不同抗稻瘟病基因间的抗性效应及抗性基因导入对受体亲本农艺性状的影响。【结果】通过对杂交后代和回交群体的Pi1、Pi2和Pigm基因相关分子标记检测,发现抗稻瘟病基因Pi1、Pi2和Pigm已成功导入到桂R1703中,筛选获得7个携带有抗稻瘟病基因且抗性和农艺性状综合表现优良的导入株系,表现出较强的稻瘟病抗性。单基因导入系中,抗稻瘟病基因的抗性效应排序为为Pigm>Pi2>Pi1;双基因和三基因导入系的稻瘟病抗性均强于单基因导入系,尤其以三基因导入系抗性最强,不同基因聚合的抗性效应排序为Pi1+Pi2+Pigm>Pi2+Pigm>Pi1+Pigm>Pi1+Pi2。7个瘟病抗性基因导入株系与桂R1703在穗长和千粒重方面无显著差异(P>0.05,下同),有2个瘟病抗性基因导入系的株高显著高于桂R1703(P<0.05,下同);有1个瘟病抗性基因导入系的单株有效穗显著高于桂R1703;有3个瘟病抗性基因导入系的单穗总粒数显著高于桂R1703;有5个瘟病抗性基因导入系结实率显著低于桂R1703;有2个瘟病抗性基因导入系的单株产量显著低于桂R1703;有4个瘟病抗性基因导入系的单株产量显著高于桂R1703。【结论】通过分子标记辅助选育可有效聚合多基因(Pi1、Pi2和Pigm基因),使恢复系桂R1703的稻瘟病抗性得到明显提升,获得一系列抗稻瘟病且与亲本其他性状相近的遗传材料,可作为亲本材料用于选育抗病优质的杂交稻。

荔枝、龙眼育种研究进展

我国是荔枝、龙眼原产国,荔枝、龙眼栽培历史悠久,野生荔枝、龙眼资源丰富.随着社会的发展,原有的荔枝、龙眼品种难以满足市场需求,选育符合市场需求的优良品种是荔枝、龙眼产业发展的迫切要求.本文综述了不同育种方法,即常规实生育种、杂交育种、分子标记辅助育种和生物技术育种运用于荔枝、龙眼的情况,并对今后荔枝、龙眼的育种发展进行了展望.

利用龙稻5号/中优早8号RIL群体定位粒形QTL

【目的】粒形是决定稻米产量、品质和商品价值的重要数量性状之一。本研究旨在利用水稻重组自交系群体鉴定控制粒形的QTL,为水稻粒形基因的挖掘和长粒形粳稻育种应用奠定基础。【方法】以短圆粒形的粳型超级稻品种龙稻5号(LD5)为母本和细长粒形的早熟籼稻品种中优早8号(ZYZ8)为父本构建包含176个家系的重组自交系群体测定粒长、粒宽、长宽比和粒厚等粒形性状,分析粒形性状间的关系并进行QTL定位和比较分析。【结果】利用区间作图法共检测到8个粒形QTL,分布在3、5、6、7和11号染色体上,表型贡献率范围为4.69%~18.89%,LOD值范围为2.52~8.74。这8个QTL包括3个粒长QTL qGL3、qGL7和qGL11,2个粒宽QTL qGW3和qGW5,2个粒厚QTL qGT3和qGT6,1个长宽比QTL qLWR3。其中,qGL3、qGL7、qGW3、qGW5和qLWR3可以在3个年份稳定检测到。利用多环境联合分析共检测到14个粒形QTL,包括qGL2、qGL3、qGL7和qGL11共4个粒长QTL;qGW3和qGW5共2个粒宽QTL;qGT3、qGT5和qGT6共3个粒厚QTL;qLWR3a、qLWR3b、qLWR5、qLWR7和qLWR11共5个长宽比QTL,分布在2、3、5、6、7和11号染色体上,表型贡献率范围为2.28%~15.78%,LOD值范围为4.20~20.90。与已克隆的粒形基因进行染色体位置比较发现,qGL3/qLWR3区间包含已克隆的GL3.1;qGW5区间包含已克隆的GW5;qLWR3b/qGT3区间包含已克隆的TGW3。【结论】利用区间作图法和多环境联合分析的方法从龙稻5号和中优早8号的重组自交系群体中共鉴定了14个粒形QTL,其中8个QTL是两种方法重复检测到的。这些QTL定位区间内包含已克隆的GL3.1、TGW3和GW5等粒形基因。

花生分子标记辅助育种研究进展与展望

花生是重要的食用植物油和植物蛋白来源,高产优质抗病是花生新品种选育的主要目标。目前生产上大面积推广的优良品种主要以传统杂交育种技术选育而成,育种周期长、效率低、成本高。分子标记辅助选择可显著提高育种的精准性和效率。高密度的基因型数据是花生产量、品质、抗病性状QTL定位和开发分子标记的基础。2019年我国花生骨干亲本狮头企和伏花生以及美国匍匐型花生品种Tifrunner的基因组序列相继公布,极大推动了花生重要农艺性状的分子标记开发和应用。近年来,花生籽仁油酸含量、脂肪含量等品质性状,根结线虫病、锈病、叶斑病、青枯病等抗病性状,以及荚果、籽仁大小等产量组成性状的分子标记相继被开发。利用分子标记辅助育种,成功选育出了高油酸且高含油量、高油酸且抗病花生新品种或新种质。未来花生分子标记的开发利用需要重视优异野生种质资源的表型精准鉴定,建立高通量表型及基因型检测平台,以及全基因组选择技术策略的应用。

烟草基因组辅助育种研究进展

优质的烟草品种是促进烟草经济发展的基础。2010年以来,烟草基因组学迅速发展,推动了烟草遗传进化、功能遗传学等多个研究领域的进步,为烟草育种提供了新的工具和途径。本文总结了烟草基因组测序组装和功能研究的最新成果,从烟草遗传连锁图谱构建、数量性状基因座(QTL)定位、全基因组关联分析(GWAS)以及QTL定位和GWAS联合分析4个方面阐述了烟草分子标记辅助选择育种(MAS)的发展现状,并综述了全基因组选择(GS)和基因编辑(GE)的技术理论以及它们在烟草育种中的应用进展。针对目前烟草基因组辅助育种(GAB)存在的问题和不足,指出要充分利用烟草基因组信息,加快分子标记的开发,推进基因芯片的应用和加强高通量表型监测平台的建设,进而推进GAB在烟草育种上的应用。

甘蓝型油菜pol CMS恢复系621R硼高效利用的遗传改良

油菜是需硼量最大的作物之一,在生产中需要额外增施硼肥,否则易出现大幅度减产。为了提高油菜对硼元素的利用效率,本研究以携带Bna.A03NIP5;1优良等位基因的硼高效利用材料2016-XFSB为供体亲本,以621R为轮回亲本,通过回交与MAS相结合的方法,将Bna.A03NIP5;1优良等位基因导入621R中,选育出拥有621R遗传背景并携带有Bna.A03NIP5;1优良等位基因的近等基因系材料621R^(NIP5;1A3),并在此基础上与细胞核雄性不育系RG430A配制了杂交种。利用水培和不同土质土壤栽培试验对621R和621R^(NIP5;1A3)及其杂种进行相关农艺性状的鉴定。结果表明,621R^(NIP5;1A3)及其杂交种对硼的利用效率有明显提升。农艺性状考察结果表明,621R^(NIP5;1A3)及其改良杂交种在生物量、株高、角果长、每角果粒数和千粒重等性状上有显著优势。本研究结果对油菜硼高效育种具有重要参考价值。

兰花分子育种技术研究进展

兰花具有很高的观赏、药用、食用、生态和文化价值,因其丰富的种类、独特多样的花型、迷人的花色、怡人的香气和神秘的起源受到各国人民的喜爱。分子育种是兰花育种的发展方向,本文对近年来兰花基因组测序、主要育种目标性状的分子遗传基础和基因克隆以及转基因、基因编辑、分子标记辅助选择育种技术等方面的研究进展进行了综述,并对未来兰花分子育种技术研究的重点和品种创新进行了展望。

A Pyramid Breeding of Eight Grain-yield Related Quantitative Trait Loci Based on Marker-assistant and Phenotype Selection in Rice(Oryza sativa L.)

1000-Grain weight and spikelet number per panicle are two important components for rice grain yield. In our previous study, eight quantitative trait loci （QTLs） conferring spikelet number per panicle and 1000-grain weight were mapped through sequencing-based genotyping of 150 rice recombinant inbred lines （RILs）. In this study, we validated the effects of four QTLs from Nipponbare using chromosome segment substitution lines （CSSLs）, and pyramided eight grain yield related QTLs. The new lines containing the eight QTLs with positive effects showed increased panicle and spikelet size as compared with the parent variety 93-11. We further proposed a novel pyramid breeding scheme based on marker-assistant and phenotype selection （MAPS）. This scheme allowed pyramiding of as many as 24 QTLs at a single hybridization without massive cross work. This study provided insights into the molecular basis of rice grain yield for direct wealth for high-yielding rice breeding.

利用胚挽救技术创制无核葡萄新材料

【目的】以无核葡萄为母本进行无核葡萄新材料创制,探明火焰无核、克伦生、红宝石无核等无核葡萄品种为母本胚培养的幼果最佳采样时间,并通过分子标记辅助育种对杂种植株的无核性状进行早期鉴定,筛选杂交F1代无核材料,提高无核葡萄育种效率。【方法】通过胚挽救技术创制无核葡萄新材料,并利用无核分子标记p3-VvAGL11、GLSP1-569、SCF27-2000、SCC8-1018等对杂种植株无核性状进行鉴定。【结果】共获得杂种植株1059株,其中以红宝石无核为母本进行胚挽救的成苗率在12.48%以上,明显高于其他品种为母本的组合;火焰无核、克伦生、红宝石无核为杂交母本时,分别在第一次授粉后38、48、55 d采集幼果的胚挽救效率最高;利用无核分子标记p3-VvAGL11、GLSP1-569、SCF27-2000、SCC8-1018对杂种植株无核性状进行鉴定,所有杂交组合杂种后代的无核率均在58%以上。【结论】红宝石无核更适合作为胚挽救育种的母本材料,火焰无核、克伦生、红宝石无核为杂交母本时,分别在第一次授粉后38、48、55 d进行幼果采集效果较好,无核分子标记p3-VvAGL11、GLSP1-569、SCF27-2000、SCC8-1018可以准确对杂种植株的无核性状进行鉴定,缩短无核葡萄育种时间。